[med-svn] r1498 - in trunk/packages: . molphy molphy/trunk molphy/trunk/debian molphy/trunk/debian/patches molphy/trunk/debian/tests molphy/trunk/debian/tests/compare
tille at alioth.debian.org
tille at alioth.debian.org
Mon Mar 3 07:16:48 UTC 2008
Author: tille
Date: 2008-03-03 07:16:47 +0000 (Mon, 03 Mar 2008)
New Revision: 1498
Added:
trunk/packages/molphy/
trunk/packages/molphy/trunk/
trunk/packages/molphy/trunk/debian/
trunk/packages/molphy/trunk/debian/FORMAT
trunk/packages/molphy/trunk/debian/PROTMLver1.DOC
trunk/packages/molphy/trunk/debian/README
trunk/packages/molphy/trunk/debian/README.Debian
trunk/packages/molphy/trunk/debian/changelog
trunk/packages/molphy/trunk/debian/compat
trunk/packages/molphy/trunk/debian/control
trunk/packages/molphy/trunk/debian/copyright
trunk/packages/molphy/trunk/debian/dirs
trunk/packages/molphy/trunk/debian/docs
trunk/packages/molphy/trunk/debian/examples
trunk/packages/molphy/trunk/debian/install
trunk/packages/molphy/trunk/debian/links
trunk/packages/molphy/trunk/debian/manpages
trunk/packages/molphy/trunk/debian/mollist.1
trunk/packages/molphy/trunk/debian/patches/
trunk/packages/molphy/trunk/debian/patches/src.diff
trunk/packages/molphy/trunk/debian/patches/src.diff_schnurps
trunk/packages/molphy/trunk/debian/patches/utl_Install.diff
trunk/packages/molphy/trunk/debian/protml.1
trunk/packages/molphy/trunk/debian/rules
trunk/packages/molphy/trunk/debian/tests/
trunk/packages/molphy/trunk/debian/tests/compare/
trunk/packages/molphy/trunk/debian/tests/compare/README.compare
trunk/packages/molphy/trunk/debian/tests/compare/test15.dis
trunk/packages/molphy/trunk/debian/tests/compare/test15.ml
trunk/packages/molphy/trunk/debian/tests/compare/test15.nj
trunk/packages/molphy/trunk/debian/tests/compare/test15.nj-2.2
trunk/packages/molphy/trunk/debian/tests/compare/test15.njo
trunk/packages/molphy/trunk/debian/tests/compare/test15.tpl
trunk/packages/molphy/trunk/debian/tests/compare/test15.tree
trunk/packages/molphy/trunk/debian/tests/compare/test4.dis
trunk/packages/molphy/trunk/debian/tests/compare/test4.ml
trunk/packages/molphy/trunk/debian/tests/compare/test4.nj
trunk/packages/molphy/trunk/debian/tests/compare/test4.nj-2.2
trunk/packages/molphy/trunk/debian/tests/compare/test4.tpl
trunk/packages/molphy/trunk/debian/tests/compare/test5.ml
trunk/packages/molphy/trunk/debian/tests/compare/test5.nj
trunk/packages/molphy/trunk/debian/tests/compare/test5.tpl
trunk/packages/molphy/trunk/debian/tests/compare/test6.ml
trunk/packages/molphy/trunk/debian/tests/compare/test6.mlq
trunk/packages/molphy/trunk/debian/tests/compare/test6.mls
trunk/packages/molphy/trunk/debian/tests/compare/test6.mls-2.2
trunk/packages/molphy/trunk/debian/tests/compare/test6.tpl
trunk/packages/molphy/trunk/debian/tests/compare/test6.tplq
trunk/packages/molphy/trunk/debian/tests/compare/test7.mlq
trunk/packages/molphy/trunk/debian/tests/compare/test7.mls
trunk/packages/molphy/trunk/debian/tests/compare/test7.mls-2.2
trunk/packages/molphy/trunk/debian/tests/compare/test7.tpl
trunk/packages/molphy/trunk/debian/tests/comparetests
trunk/packages/molphy/trunk/debian/tests/makefile
trunk/packages/molphy/trunk/debian/tests/test15.cns
trunk/packages/molphy/trunk/debian/tests/test15.ptn
trunk/packages/molphy/trunk/debian/tests/test15.tree
trunk/packages/molphy/trunk/debian/tests/test4.ptn
trunk/packages/molphy/trunk/debian/tests/test5.ptn
trunk/packages/molphy/trunk/debian/tests/test6.nuc
trunk/packages/molphy/trunk/debian/tests/test7.ptn
Log:
Molphy moved to group maintenance
Added: trunk/packages/molphy/trunk/debian/FORMAT
===================================================================
--- trunk/packages/molphy/trunk/debian/FORMAT (rev 0)
+++ trunk/packages/molphy/trunk/debian/FORMAT 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,226 @@
+
+ Format of Input SEQUENCES File
+
+
+ standard MOLPHY input sequence data format:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+4 90
+Data1
+MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMKPTLLTATSVFIIAFIHAPPVDK
+DGHREPVSGSGRVINTWADIINRANLGMEV
+Data2
+MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMKPTLLTATICFIIAFIHAPPVDK
+DGHREPVAGSGRVISTWADILNRANLGFEV
+Data3
+MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMKPTLLTATICFIVAFIHAPPVDK
+DGHREPVAGSGRVINTWADVLNRANLGMEV
+Data4
+MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMKPTLLAATACFVIAFIHAPPVDK
+DGHREPVAGSGRVIATWADVINRANLGMEV
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Note, "~~~" is file separater.
+
+An input file has two parts of data; SIZE and SEQUENCES.
+
+1. SIZE
+The first line of the file contains the number of species(OTUs) and the length
+of amino acid sequences, in free format, separated by blanks(space or tab).
+You can write comment of the data after two digits numbers,
+separated by blanks.
+
+2. SEQUENCES
+The following lines give sets of species name and amino acid sequence data.
+Names are made up of letters and digits; the first character must be a letter.
+The underscore "_" is regarded as a letter. Upper case and lower case letters are
+distinct, so "spc_1", "Spc_1" and "SPC_1" are three different names.
+Name can NOT include blanks.
+You must put the amino acid sequence AFTER NEWLINE in free format.
+Separated by whitespace(space, tab or newline) is allowed.
+The amino acids must be specified by the one letter codes adopted by
+IUPAC-IUB Commission on Biochemical Nomenclature (1968).
+
+ CODE Amino acid Description
+ A Ala Alanine
+ R Arg Arginine
+ N Asn Asparagine
+ D Asp Aspartic acid
+ C Cys Cysteine
+ Q Gln Glutamine
+ E Glu Glutamic acid
+ G Gly Glycine
+ H His Histidine
+ I Ile Isoleucine
+ L Leu Leucine
+ K Lys Lysine
+ M Met Methionine
+ F Phe Phenylalanine
+ P Pro Proline
+ S Ser Serine
+ T Thr Threonine
+ W Trp Tryptophan
+ Y Tyr Tyrosine
+ V Val Valine
+ B Asx Aspartic acid or Asparagine
+ Z Glx Glutamine or Glutamic acid
+ X Xaa Any amino acid
+ - gap Ins/Del
+
+
+ Felsenstein's PHYLIP "SEQUENTIAL" format:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ 4 90
+Data1 MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFII
+AFIAAPPVDIDGIREPVSGSGRVINTWADIINRANLGMEV
+Data2 MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFII
+AFIAAPPVDIDGIREPVAGSGRVISTWADILNRANLGFEV
+Data3 MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIV
+AFIAAPPVDIDGIREPVAGSGRVINTWADVLNRANLGMEV
+Data4 MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVI
+AFIAAPPVDIDGIREPVAGSGRVIATWADVINRANLGMEV
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The information for each species follows, starting with a TEN-CHARACTER
+species name (which CAN include punctuation marks and blanks).
+You must use SEQUENTIAL_FILE with "-S" Switch, follow as:
+
+ protml -S SEQUENTIAL_FILE
+
+
+ MOLPHY and PHYLIP common format:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ 4 90$
+Data1 $
+MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDI$
+DGIREPVSGSGRVINTWADIINRANLGMEV$
+Data2 $
+MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFIIAFIAAPPVDI$
+DGIREPVAGSGRVISTWADILNRANLGFEV$
+Data3 $
+MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIVAFIAAPPVDI$
+DGIREPVAGSGRVINTWADVLNRANLGMEV$
+Data4 $
+MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVIAFIAAPPVDI$
+DGIREPVAGSGRVIATWADVINRANLGMEV$
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Note, '$' is newline(return) code.
+
+
+ PHYLIP and other packages "INTERLEAVED" format:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ 4 90
+Data1 MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFII
+Data2 MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFII
+Data3 MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIV
+Data4 MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVI
+
+AFIAAPPVDIDGIREPVSGSGRVINTWADIINRANLGMEV
+AFIAAPPVDIDGIREPVAGSGRVISTWADILNRANLGFEV
+AFIAAPPVDIDGIREPVAGSGRVINTWADVLNRANLGMEV
+AFIAAPPVDIDGIREPVAGSGRVIATWADVINRANLGMEV
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+You must use INTERLEAVED_FILE with "-I" Switch, follow as:
+
+ protml -I INTERLEAVED_FILE
+
+
+
+ Format of USERS TREES File
+
+ standard USERS TREES file format:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+3
+(((HUMAN,(CHIMP,PYGMY)),GORIL),ORANG,SIAMA);
+((HUMAN,((CHIMP,PYGMY),GORIL)),ORANG,SIAMA);
+(((HUMAN,GORIL),(CHIMP,PYGMY)),ORANG,SIAMA);
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Note, "~~~" is file separater.
+
+An input file has two parts of data; SIZE and MACHINE READABLE TREES.
+
+1. SIZE
+The first line of the file contains the number of machine readable trees.
+You can write comment of the trees after one digits number,
+separated by blanks(space or tab).
+
+2. MACHINE READABLE TREES
+The following lines give sets of (user-defined) machine readable tree.
+The tree is specified by the nested pairs of parentheses, enclosing names
+and separated by commas. Semicolon ";" is tree terminator.
+The pattern of the parentheses represents the tree topology by having
+each pair of parentheses enclose all the members of a monophyletic group.
+You must put the next machine readable tree AFTER NEWLINE in free format,
+allow separated by whitespace(space, tab or newline).
+for example,
+
+ (((HUMAN,(CHIMP,PYGMY)),GORIL),ORANG,SIAMA);
+
+ (
+ (
+ (
+ HUMAN,
+ (
+ CHIMP,
+ PYGMY
+ )
+ ),
+ GORIL
+ ),
+ ORANG,
+ SIAMA
+ );
+
+the above two machine readable tree are the same.
+
+Note that the machine readable tree is an UNROOTED one, and therefore its base
+must be multifurcation with a multiplicity of greater than or equal to three.
+
+ Unrooted tree (PROTML & DISTNJ) Rooted tree (not allowed)
+ variable rate constant rate
+
+ ( subtree1, subtree2, subtree3 ); ( subtree1, subtree2 );
+
+ :-----subtree1
+ : :-----subtree1
+ :-----subtree2 :
+ : :-----subtree2
+ :-----subtree3
+ ^root
+ ^provisional root
+
+
+
+ Format of CONSTRAINED TREE File
+
+
+ standard CONSTRAINED TREE file format:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+( { HUMAN,CHIMP,PYGMY,GORIL }, ORANG, SIAMA );
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Note, "~~~" is file separater.
+
+CONSTRAINED TREE file allow constrained machine readable tree.
+Pair of PARENTHESIS indicates FIX tree structure, but Pair of BRACE indicates
+COMBINATION tree structure in a monophyletic group.
+
+above CONSTRAINED TREE input PROTML with "-e" switch
+
+ protml -e sequence_file constrained_tree
+
+automatic generation of all possible trees.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+15
+(((HUMAN,(CHIMP,PYGMY)),GORIL),ORANG,SIAMA);
+((HUMAN,((CHIMP,PYGMY),GORIL)),ORANG,SIAMA);
+(((HUMAN,GORIL),(CHIMP,PYGMY)),ORANG,SIAMA);
+((((HUMAN,PYGMY),CHIMP),GORIL),ORANG,SIAMA);
+((((HUMAN,CHIMP),PYGMY),GORIL),ORANG,SIAMA);
+((HUMAN,(CHIMP,(PYGMY,GORIL))),ORANG,SIAMA);
+((HUMAN,((CHIMP,GORIL),PYGMY)),ORANG,SIAMA);
+((((HUMAN,GORIL),PYGMY),CHIMP),ORANG,SIAMA);
+((((HUMAN,CHIMP),GORIL),PYGMY),ORANG,SIAMA);
+(((HUMAN,CHIMP),(PYGMY,GORIL)),ORANG,SIAMA);
+((((HUMAN,GORIL),CHIMP),PYGMY),ORANG,SIAMA);
+(((HUMAN,(PYGMY,GORIL)),CHIMP),ORANG,SIAMA);
+(((HUMAN,(CHIMP,GORIL)),PYGMY),ORANG,SIAMA);
+(((HUMAN,PYGMY),(CHIMP,GORIL)),ORANG,SIAMA);
+((((HUMAN,PYGMY),GORIL),CHIMP),ORANG,SIAMA);
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Added: trunk/packages/molphy/trunk/debian/PROTMLver1.DOC
===================================================================
--- trunk/packages/molphy/trunk/debian/PROTMLver1.DOC (rev 0)
+++ trunk/packages/molphy/trunk/debian/PROTMLver1.DOC 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,682 @@
+
+ PROTML version 1 ( old version )
+ Maximum Likelihood Inference of Protein Phylogeny
+
+
+ Jun Adachi 1) and Masami Hasegawa 2)
+
+
+ 1) Department of Statistical Science,
+ The Graduate University for Advanced Study
+ 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan
+
+ 2) The Institute of Statistical Mathematics
+ 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan
+
+
+
+ INTRODUCTION
+
+
+ PROTML is a PASCAL program for inferring evolutionary trees
+from protein (amino acid) sequences by using maximum likelihood.
+
+ A maximum likelihood method for inferring trees from DNA or
+RNA sequences was developed by Felsenstein (1981). The method
+does not impose any constraint on the constancy of evolutionary
+rate among lineages. He wrote a program (DNAML) implementing the
+method, and included it in his program package, PHYLIP. The
+program has been used extensively and has proved of great use in
+phylogenetic studies (Hasegawa and Yano, 1984a; Hasegawa et al.,
+1985, 1990a; Hasegawa and Kishino, 1989; Kishino and Hasegawa,
+1989; Zillig et al., 1989; Hasegawa, 1990, 1991; Golenberg et
+al., 1990; Adkins and Honeycutt, 1991; Doebley et al., 1991;
+Edwards et al., 1991; Les et al., 1991; Ruvolo et al., 1991;
+Disotell et al., 1992; Lockhart et al., 1992). Computer
+simulations have demonstrated that the method is highly efficient
+in estimating a true tree under various situations such as a
+violation of rate constancy among lineages (Hasegawa and Yano,
+1984b; Hasegawa et al., 1991).
+
+ DNAML, however, is confined to DNA or RNA sequence data, and
+is not applicable to protein sequence data. In phylogenetic
+studies of deep branchings, such as those among the three major
+kingdoms of eukaryotes, archaebacteria and eubacteria, and those
+in the early evolution of eukaryotes, ribosomal RNA sequence data
+has been used widely (e.g., Woese, 1989; Sogin et al., 1989). In
+spite of many works on the ribosomal RNAs, the universal root of
+all contemporary organisms on the earth including eukaryotes,
+archaebacteria and eubacteria remained uncertain. Miyata and his
+coworkers demonstrated the usefulness of using amino acid
+sequence data encoded by duplicated genes (duplicated prior to
+the divergence among the major kingdoms) in establishing the
+universal root (Iwabe et al., 1989; Hasegawa et al., 1990b;
+Miyata et al., 1991). Furthermore, an evolutionary tree inferred
+from ribosomal RNA data is sometimes misleading when base
+composition differs widely among lineages, and a tree inferred
+from protein sequences is more reliable in such cases (Loomis and
+Smith, 1990; Hasegawa et al., 1993).
+
+ Because no program was available for inferring a protein
+tree by maximum likelihood based on a reasonable model of amino
+acid substitutions, many authors used DNAML in analyzing
+protein-encoding DNA sequences. As is well known, the third
+position of codons evolve more rapidly than other positions, and
+therefore DNAML was designed so that a user could specify the
+relative rates of substitutions in several categories of
+positions. This approach seems to be good in many cases when one
+is interested in phylogenetic relationships among closely related
+species.
+
+ Even if the rate difference among positions in a codon are
+taken into account, however, inclusion of the third positions in
+the analysis can sometimes be misleading when the pattern of
+codon usage differs among lineages. Furthermore, the assumption
+(in DNAML) of independent evolution among three positions of a
+codon can be a serious defect when one is interested in tracing
+deep branchings, because a (negative) selection is likely to be
+operating at the codon level, rather than at the individual sites
+in the codon. Even if nucleotide frequencies of protein-encoding
+genes differ among lineages, amino acid frequencies may not
+differ significantly (Adachi and Hasegawa, 1992). Therefore, if
+the amino acid substitution process can be represented by an
+appropriate model, it seems to be better to handle amino acid
+sequences rather than nucleotide sequences in estimating orders
+of deep branchings from data of a protein-encoding gene, and
+there is an increasing demand for a maximum likelihood program to
+infer protein phylogenies.
+
+ Kishino et al. (1990) developed a maximum likelihood method
+for inferring protein phylogenies that takes account of unequal
+transition probabilities among pairs of amino acids by using an
+empirical transition matrix compiled by Dayhoff et al. (1978),
+and the model is called the Dayhoff model (Hasegawa et al.,
+1992). Although the transition matrix was constructed from a
+limited data set (accumulated up to 1978) of proteins encoded in
+nuclear DNA, the Dayhoff model is not necessarily specific only
+to those proteins, but is appropriate in approximating the amino
+acid substitutions of wider protein species including
+mitochondrial ones (Hasegawa et al., 1993; Adachi and Hasegawa,
+1992; Adachi et al., 1992).
+
+ The original program for private use in Kishino et al.
+(1990), Mukohata et al. (1990), Hasegawa et al. (1990b), Iwabe et
+al. (1991), and Miyata et al. (1991) was written in FORTRAN and
+the number of species in the maximum likelihood analysis was
+confined to five. In writing this program "PROTML" for public
+use, we took advantage of another computer language, PASCAL, to
+represent the tree structure of the data. In this program, there
+is no limit on the number of species, provided the computer is
+big enough.
+
+ Since the number of possible tree topologies increases
+explosively as the number of species increases (Felsenstein,
+1978a), it is a serious problem to find the best tree among the
+huge number of alternatives. We have developed a novel algorithm
+for searching tree topologies, called "star decomposition", which
+seems to be effective in finding the best tree.
+
+ The parsimony method has been used widely in molecular
+phylogenetics, but it may be positively misleading when the
+evolutionary rate differs among lineages (Felsenstein, 1978b).
+PROTML has proved of great use in inferring evolutionary trees
+even in such situations (Hasegawa et al., 1992), and has been
+applied to several phylogenetic problems (Hasegawa et al., 1993;
+Adachi and Hasegawa, 1992; Adachi et al., 1992; Hashimoto et al.,
+1993).
+
+ The overall structure of PROTML is similar to that of
+Felsenstein's DNAML. We owe very much to DNAML in the writing
+PROTML, and have adopted several fundamental routines from the
+DNAML program. Furthermore, the input format of PROTML is quite
+similar to that of DNAML. Features where PROTML differs from
+DNAML (up to version 3.4) are as follows:
+
+ (1) Amino acid sequence data are analyzed based on Dayhoff's
+ model(1978).
+ (2) The likelihood of multifurcating trees can be estimated.
+ (3) A novel method of topology search ("star decomposition")
+ is adopted.
+ (4) The Newton method is adopted in the maximization of
+ likelihood.
+ (5) Bootstrap probabilities of candidate trees can be
+ estimated.
+
+
+
+ ALGORITHM FOR TOPOLOGY SEARCH
+
+ Topological Data Structure
+
+ Felsenstein considered a data structure representing the
+unrooted tree, where each internal node (excluding external nodes
+or tips) is decomposed into elements, the number of which
+coincides with those of branches stemming from the node. The
+elements are connected circularly through the pointers.
+
+ By adopting such a data structure, we can store a partial
+likelihood of a sub-tree stemming from the node. This means that,
+when we estimate the likelihood of the tree, we need not
+calculate likelihood through iteration of a loop by the times of
+the number of nodes in revising the estimate of each branch
+length, but need only revise the partial likelihoods of two nodes
+of each branch.
+
+ We extend this data structure so that a multifurcating tree
+can be represented. Since branches are connected dynamically by
+pointers, the data structure can easily be revised when a
+different tree topology is adopted, and furthermore not only
+bifurcating trees but also multifurcating trees can be
+represented quite easily. The extreme limit of a multifurcating
+tree is the star-like tree.
+
+
+ Automatic Topology Search by Star Decomposition
+
+ The straightforward approach to inferring a tree would be to
+evaluate all possible tree topologies one after another and pick
+the one which gives the highest likelihood. This would not be
+possible for more than a small number of species, since the
+number of possible tree topologies is enormous (Felsenstein,
+1978a).
+
+ The strategy that Felsenstein's DNAML employs is as follows:
+the species are taken in the order in which they appear in the
+input file. The first three are taken and an unrooted tree is
+constructed containing only those three. Then, the fourth species
+is taken, and it is evaluated to see where it might best be added
+to the tree. All possibilities (bifurcating trees) for adding the
+fourth species are examined. The best one under the likelihood
+criterion is chosen to be the basis for further operations. Then
+the fifth species is added, and again the best placement of it is
+chosen, and so on. At each step, local rearrangements of a tree
+are examined. This procedure is continued until a bifurcating
+tree connecting all the species is obtained (Felsenstein, 1992).
+
+ The resulting tree from this procedure generally depends on
+the order of the input species. Hence, Felsenstein recommends
+performing a number of runs with different orderings of the input
+species.
+
+ The alternative strategy which we employ in the automatic
+and semi-automatic search options of PROTML is called "star
+decomposition". This is similar to the procedure employed in the
+neighbor-joining method using a distance matrix (Saitou and Nei,
+1987). This method starts with a star-like tree. Decomposing the
+star-like tree step by step, we finally obtain a bifurcating tree
+if all multifurcations can be resolved with statistical
+confidence. Since the information from all of the species under
+analysis is used from the beginning, the inference of the tree
+topology is likely to be stable by this procedure.
+
+ Let be the number of species under analysis. At first, a
+star-like tree containing species is constructed. Then, a pair of
+species is separated from others. Among all possible pairwise
+combinations of species, a pairing that gives the highest
+likelihood is chosen. The resulting tree can be regarded as a
+star-like tree with groups (a single species may form a group),
+if the selected pair is regarded to form a group. This procedure
+is continued until all multifurcating nodes are resolved into
+bifurcating ones.
+
+ When the information content of the data is not large enough
+to discriminate among alternative branching orders, it might be
+misleading to resolve all the multifurcations into bifurcations.
+Hence, by using "Akaike Information Criteria (AIC)" (Akaike,
+1974), the program decides whether the multifurcation should
+further be resolved or not.
+
+
+
+ PROTML USER'S GUIDE
+
+ Options
+
+ The program allows various options that alter the amount of
+information the program is provided or what it is to be done with
+the information. The program is notified that an option has been
+invoked by the presence of one or more letters after the last
+number on the first line of the input file. These letters may or
+may not be separated from each other by blanks, though it is
+usually necessary to separate them from the number by a blank.
+They can be in any order. Thus to invoke options U, W and B, the
+input file starts with the line:
+
+ 19 409 UWB
+
+or
+
+ 19 409 W U B
+
+ This program has three mode of topology search; i.e.,
+Automatic mode, Semi-automatic mode and User tree (manual) mode.
+
+ Automatic mode.
+ Unless specified otherwise, the procedure uses automatic mode,
+ so it starts with a star-like tree.
+
+ "S" : Semi-automatic mode.
+ Semi-automatic mode starts with a multifurcating tree that a
+ user designates.
+
+ "U" : User tree mode.
+ User tree (manual) mode is similar to the "U" option in
+ Felsenstein's DNAML. This mode calculates the likelihood of
+ all user defined topologies. Different from DNAML, this
+ program allows multifurcating trees as user trees.
+
+ "W" : Write option.
+ Using this option, the program will produce more information
+ than it dose for standard output.
+
+ "B" : Bootstrap option.
+ This option gives the approximate bootstrap probabilities of
+ candidate trees by a resampling of estimated likelihood (RELL)
+ method (Kishino et al., 1990).
+
+
+ Format of input data file
+
+ We have tried to adhere to a rather stereotyped input format
+similar to that of Felsenstein's programs. The simplest version
+of the input file looks something like this:
+
+ 4 40 W
+ species1 ARNDCQEGHILKAFPMTWYVARNDCQEGHISKMFGWTWYV
+ species2 ARNHNQCGHILKMFPMTSYVARNCCAEHHILKHFPSTWIV
+ species3 AINDCQEGHHLKMFPMTMYSVRNRIQEMHIQKHCPHTHYV
+ species4 AINHCQCEHILWMFPSTPYVARNDIQNYHILKMPPSTWWV
+
+ The first line of the input file contains the number of
+species and the length of amino acid sequences, in free format,
+separated by blanks. The information for each species follows,
+starting with a ten-character species name (which can include
+punctuation marks), and continuing with the characters for that
+species.
+
+ An input file has three parts of data; i.e., arguments,
+sequences and topologies.
+
+ 1. Arguments
+ The first line of the file gives number of species, sequence
+ length, and options.
+
+ 2. Sequences
+ The following lines give species names and amino acid sequence
+ data. The amino acids must be specified by the one letter
+ codes adopted by IUPAC-IUB Commission on Biochemical
+ Nomenclature (1968). The amino acid code must be one of the
+ twenty.
+
+ 3. Topologies
+ If one specifies User or Semi-automatic options, one mast
+ specify the number of topologies followed by the topologies
+ themselves.
+
+ This program allows the option U, which signals that user-
+defined tree(s) are provided. The topologies of these trees are
+supplied AFTER the species and sequence data, rather than before
+them. The letter U appears on the first line of the file. After
+the species and sequence data, a line containing the number of
+user-defined trees appears. Each user-defined tree starts on a
+new line. Here is an example with three user-defined trees:
+
+ 5 40 U B
+ species1 ARNDCQEGHILKAFPMTWYVARNDCQEGHISKMFGWTWYV
+ species2 ARNHNQCGHILKMFPMTSYVARNCCAEHHILKHFPSTWIV
+ species3 AINDCQEGHHLKMFPMTMYSVRNRIQEMHIQKHCPHTHYV
+ species4 AINHCQCEHILWMFPSTPYVARNDIQNYHILKMPPSTWWV
+ species5 AINDCSCGHHLWMFPSLCYVRRNECQGGHIWKMFPLTVCA
+ 3
+ (((species1,species2),species3),species4,species5)
+ ((species1,species2),(species3,species4),species5)
+ (species1,(species2,species3),(species4,species5))
+
+ An example of semi-auto mode is as follows:
+
+ 5 40 S
+ species1 ARNDCQEGHILKAFPMTWYVARNDCQEGHISKMFGWTWYV
+ species2 ARNHNQCGHILKMFPMTSYVARNCCAEHHILKHFPSTWIV
+ species3 AINDCQEGHHLKMFPMTMYSVRNRIQEMHIQKHCPHTHYV
+ species4 AINHCQCEHILWMFPSTPYVARNDIQNYHILKMPPSTWWV
+ species5 AINDCSCGHHLWMFPSLCYVRRNECQGGHIWKMFPLTVCA
+
+ ((species1,species2,species3),species4,species5)
+
+ The tree topology is specified by nested pairs of
+parentheses, enclosing species names and separated by commas.
+Trailing blanks in the name may be omitted. The pattern of the
+parentheses indicates the pattern of the tree by having each pair
+of parentheses enclose all the members of a monophyletic group.
+The entire tree is enclosed in an outermost pair of parentheses.
+Note that the tree is an unrooted one, and therefore its base
+must be multifurcation with a multiplicity of greater than or
+equal to three. A specification of a tree ends with a semicolon
+which may be omitted.
+
+
+ Program Constants
+
+ The CONSTants in program that may be changed by a user are:
+
+ CONST
+ maxsp : maximum number of species
+ maxnode : maxsp * 2 - 3
+ maxpair : maxsp * (maxsp-1) / 2
+ maxsite : maximum number of sites
+ maxptrn : maximum number of different site patterns
+ maxtree : maximum number of user trees
+ maxsmooth : number of smoothing algorithm
+ maxiterat : number of iterates of Newton method
+ epsilon : stopping value of error
+ minarc : lower limit on number of substitutions per branch
+ maxarc : upper limit on number of substitutions per branch
+ prprtn : proprtion of branch length
+ maxboot : number of bootstrap replications
+ maxexe : number of jobs
+ maxline : length of sequence output per line
+ maxname : maximum number of characters in species name
+ maxami : number of amino acids
+ minreal : if job is in underflow error, increase this value
+ seqfname : input file of sequence data
+ tpmfname : input file of transition probability
+ lklfname : output file of log-likelihood
+
+
+ Output Format
+
+ The output usually consists of
+ (1) the name of the program and its version number,
+ (2) the input information printed out, and
+ (3) a series of trees,
+some with associated information indicating how much change there
+was in each character or on each part of the tree.
+
+ The tree grows from left to right and has branches that are
+approximately proportional in length to the lengths that the
+program estimates. In some cases when branches are estimated to
+be very short, the output makes them three spaces long so that
+the topology is clearly shown. Here is what a typical tree looks
+like:
+
+ :-----------1.Tabac.chl
+ 0:
+ : :-------2.Prochloro
+ : :----6
+ : : :---3.Anacystis
+ :---7
+ : :------------------5.Synechocy
+ :
+ :------4.Fremyella
+
+ No. number Length S.E.
+ ----------------------------------------------
+ Tabac.chl 1 9.44861 ( 1.63423 )
+ Prochloro 2 5.69634 ( 1.30862 )
+ Anacystis 3 1.57704 ( 0.74325 )
+ Fremyella 4 4.92061 ( 1.24297 )
+ Synechocy 5 16.05818 ( 2.24639 )
+ 6 2.13260 ( 0.86082 )
+ 7 1.01070 ( 0.63908 )
+ ----------------------------------------------
+ ln L : -1813.614 ( 66.205 ) AIC : 3641.229
+ ----------------------------------------------
+
+ Length refers to the estimated number of substitutions per
+100 amino acid sites along the branch leading to the node (or
+leaf) indicated by the number, and S.E. refers to its standard
+error estimated by the formula of Kishino and Hasegawa (1989).
+
+
+
+ Installing PROTML and Executive Environment
+
+
+ Personal computer with MS-DOS + Turbo Pascal(Borland): e.g.
+IBM PCs and compatibles, NEC PC-98x. Please remove or change
+comments marked as shown below:
+
+ (* <statements> TURBO Pascal *)
+
+ UNIX Workstation + standard Pascal compiler: e.g. SUN.
+Please remove or change comments marked as shown below:
+
+ (* <statements> SUN Pascal *)
+
+ Mainframe computer (IBM and compatibles) + standard Pascal
+compiler. For example, JCL (Job Control Language) of batch job.
+
+ //USERIDB JOB PATHWORD
+ //STEP EXEC OPASCLG
+ //PASC.SYSIN DD DSN='USERID.PROTML.PASCAL',DISP=SHR
+ //GO.SEQFILE DD DSN='USERID.SEQFILE.DATA',DISP=SHR
+
+
+
+ How to contact developers
+
+
+ The best way to contact developers is to send an E-mail.
+
+ E-mail: adachi at ism.ac.jp
+
+If you prefer, write a letter with your comments and send it to
+
+ Jun Adachi
+ Department of Statistical Science,
+ The Graduate University for Advanced Study,
+ 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan
+ FAX: +81-3-3446-1695
+
+ Please send a mail with the following information
+
+ 1. Computer brand, model.
+ 2. The brand and version number of Pascal compiler.
+ 3. Operating system and version number.
+ 4. The input file of sequence data.
+ 5. The output file.
+
+
+
+ Acknowledgements
+
+
+ We are particularly grateful to Dr. H. Kishino for
+invaluable advices during the course of this work, and to Dr. J.
+Felsenstein for generously permitting us to use routines in
+DNAML. We also thank Drs. T. Hashimoto, T. Miyata and T. Yano for
+discussions and comments. This work was carried out under the
+Institute of Statistical Mathematics Cooperative Research Program
+(90-ISM-57, 91-ISM-69), and was supported by grants from the
+Ministry of Education, Science, and Culture of Japan.
+
+
+
+ References
+
+
+Adachi, J., Hasegawa, M. (1992)
+ Amino acid substitution of proteins coded for in mitochondrial
+DNA during mammalian evolution. Jpn. J. Genet., 67:187-197.
+
+Adachi, J., Cao, Y., Hasegawa, M. (1993)
+ Tempo and mode of mitochondrial DNA evolution in vertebrates at
+the amino acid sequence level: rapid evolution in warm-blooded
+vertebrates. J. Mol. Evol., 36:270-281.
+
+Adkins, R.M., Honeycutt, R.L. (1991)
+ Molecular phylogeny of the superorder Archonta. Proc. Natl.
+Acad. Sci. US., 88:10317-10321.
+
+Akaike, H. (1974)
+ A new look at the statistical model identification. IEEE Trans.
+Autom. Contr., 19:716-723.
+
+Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978)
+ A model of evolutionary change in proteins. In: Dayhoff, M.O.
+(ed.) Atlas of Protein Sequence Structur., Vol~5, Suppl~3.
+National Biomedical Research Foundation, Washington DC, pp.~345-
+352.
+
+Disotell, T.R., Honeycutt, R.L., Ruvolo, M. (1992)
+ Mitochondrial DNA phylogeny of the Old-World monkey tribe
+Papionini. Mol. Biol. Evol., 9:1-13.
+
+Doebley, J., Durbin, M., Golenberg, E.M., Clegg, M.T., Ma D.-P.
+(1990)
+ Evolutionary analysis of the large subunit of carboxylase ( rbc
+L) nucleotide sequence among the grasses (Gramineae). Evolutio.,
+44:1097-1108.
+
+Edwards, S.V., Arctander, P., Wilson, A.C. (1991)
+ Mitochondrial resolution of a deep branch in the genealogical
+tree for perching birds. Proc. Roy. Soc. Londo., B243:99-107.
+
+Felsenstein. J. (1978a)
+ The number of evolutionary trees. System. Zool., 27:27-33.
+
+Felsenstein. J. (1978b)
+ Cases in which parsimony and compatibility methods will be
+positively misleading. System. Zool., 27:401-410
+
+Felsenstein, J. (1981)
+ Evolutionary trees from DNA sequences: a maximum likelihood
+approach. J. Mol. Evol., 17:368-376
+
+Felsenstein, J. (1985)
+ Confidence limits on phylogenies: an approach using the
+bootstrap. Evolutio., 39:783-791.
+
+Felsenstein, J. (1992)
+ Phylogenies from restriction sites: a maximum-likelihood
+approach. Evolutio., 46:159-173.
+
+Golenberg, E.M., Giannasi, D.E., Clegg, M.T., Smiley, C.J.,
+Durbin, M., Henderson, D., Zurawski, G. (1990)
+ Chlorolplast DNA sequence from a Miocene Magnolia species.
+Natur., 344:656-658.
+
+Hasegawa, M., Yano, T. (1984a)
+ Phylogeny and classification of Hominoidea as inferred from DNA
+sequence data. Proc. Japan Acad., B60:389-392.
+
+Hasegawa, M., Yano, T. (1984b)
+ Maximum likelihood method of phylogenetic inference from DNA
+sequence data. Bull. Biomet. Soc. Jp., 5:1-7.
+
+Hasegawa, M., Iida, Y., Yano, T., Takaiwa, F., Iwabuchi, M.
+(1985)
+ Phylogenetic relationships among eukaryotic kingdoms inferred
+from ribosomal RNA sequences. J. Mol. Evol., 22:32-38.
+
+Hasegawa, M., Kishino, H. (1989)
+ Confidence limits on the maximum-likelihood estimate of the
+hominoid tree from mitochondrial- DNA sequences. Evolutio.,
+43:672-677.
+
+Hasegawa, M. (1990)
+ Phylogeny and molecular evolution in primates. Jpn. J. Genet.,
+65:243-265.
+
+Hasegawa, M. (1991)
+ Molecular phylogeny and man's place in Hominoidea. J. Anthrop.
+Soc. Nippo., 99:49-61.
+
+Hasegawa, M., Kishino, H., Hayasaka, K., Horai, S. (1990a)
+ Mitochondrial DNA evolution in primates: Transition rate has
+been extremely low in lemur. J. Mol. Evol., 31:113-121.
+
+Hasegawa, M., Iwabe, N., Mukohata, Y., Miyata, T. (1990b)
+ Close evolutionary relatedness of archaebacteria, Methanococcus
+and Halobacteriu., to eukaryotes demonstrated by composite
+phylogenetic trees of elongation factors EF-Tu and EF-G: eocyte
+tree is unlikely. Jpn. J. Genet., 65:109-114.
+
+Hasegawa, M., Kishino, H., Saitou, N. (1991)
+ On the maximum likelihood method in molecular phylogenetics. J.
+Mol. Evol., 32:443-445.
+
+Hasegawa, M., Cao, Y., Adachi, J., Yano, T. (1992)
+ Rodent polyphyly? Natur., 355:595-595.
+
+Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N., Miyata, T.
+(1993)
+ Early divergences in the evolution of eukaryotes: ancient
+divergence of Entamoeba that lacks mitochondria revealed by
+protein sequence data. J. Mol. Evol., 36:380-388.
+
+Hashimoto, T., Otaka, E., Adachi, J., Mizuta, K., Hasegawa, M.
+(1993)
+ The giant panda is most close to a bear, judged by - and
+-hemoglobin sequences. J Mol Evol. 36:282-289.
+
+IUPAC-IUB Commission on Biochemical Nomenclature (1968)
+ A one-letter notation for amino acid sequences, tentative rules.
+J. Biol. Chem., 243:3557-3559.
+
+
+Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., Miyata, T. (1989)
+ Evolutionary relationship of archaebacteria, eubacteria, and
+eukaryotes inferred from phylogenetic trees of duplicated genes.
+Proc. Natl. Acad. Sci. US., 86:9355-9359.
+
+Iwabe, N., Kuma, K., Kishino, H., Hasegawa, M., Miyata, T. (1991)
+ Evolution of RNA polymerases and branching patterns of the three
+major groups of archaebacteria. J. Mol. Evol., 32:70-78.
+
+Kishino, H., Hasegawa, M. (1989)
+ Evaluation of the maximum likelihood estimate of the
+evolutionary tree topologies from DNA sequence data, and the
+branching order in Hominoidea. J. Mol. Evol., 29:170-179.
+
+Kishino, H., Miyata, T., Hasegawa, M. (1990)
+ Maximum likelihood inference of protein phylogeny and the origin
+of chloroplasts. J. Mol. Evol., 30:151-160.
+
+Les, D.H., Garvin, D.K., Wimpee, C.F. (1991)
+ Molecular evolutionary history of ancient aquatic angiosperms.
+Proc. Natl. Acad. Sci. US., 88:10119-10123.
+
+Lockhart, P.J., Howe, C.J., Bryant, D.A., Beanland, T.J., Larkum,
+A.W.D. (1992)
+ Substitutional bias confounds inference of cyanelle origins from
+sequence data. J. Mol. Evol., 34:153-162.
+
+Loomis, W.F., Smith, D.W. (1990)
+ Molecular phylogeny of Dictyostelium discoideum by protein
+sequence comparison. Proc. Natl. Acad. Sci. US., 87:9093-9097.
+
+Miyata, T., Iwabe, N., Kuma, K., Kawanishi, Y., Hasegawa, M.,
+Kishino, H., Mukohata, Y., Ihara, K., Osawa, S. (1991)
+ Evolution of archaebacteria: Phylogenetic relationships among
+archaebacteria, eubacteria, and eukaryotes. In: Osawa, S., Honjo,
+T. (eds.) Evolution of Life: Fossils, Molecules, and Culture .
+Springer-Verlag, Tokyo, pp. 337-351.
+
+Mukohata, Y., Ihara, K., Kishino, H., Hasegawa, M., Iwabe, N.,
+Miyata, T. (1990)
+ Close evolutionary relatedness of archaebacteria with
+eukaryotes. Proc. Japan Acad., B66:63-67.
+
+Saitou, N, Nei, M. (1987)
+ The neighbor-joining method: a new method for reconstructing
+phylogenetic trees. Mol. Biol. Evol., 4:406-425.
+
+Ruvolo, M., Disotell, T.R., Allard, M.W., Brown, W.M., Honeycutt,
+R.L. (1991)
+ Resolution of the African hominoid trichotomy by use of a
+mitochondrial gene sequence. Proc. Natl. Acad. Sci. US.,
+88:1570-1574.
+
+Sogin, M.L., Edman, U., Elwood, H. (1989)
+ A single kingdom of eukaryotes.
+ In: Fernholm, B., Bremer, K., J rnvall, H. (eds.) The Hierarchy
+of Life . Elsevier Science Publisher, Amsterdam, pp. 133-143.
+
+Woese, C.R. (1989)
+ Bacterial evolution. Microbiol. Rev., 51:221-271.
+
+Zillig, W., Klenk, H.-P., Palm, P., Leffers, H., P hler, G.,
+Gropp, F., Garrett, R.A. (1989)
+ Did eukaryotes originate by a fusion event? Endocytobiosis Cell
+Res., 6:1-25
Added: trunk/packages/molphy/trunk/debian/README
===================================================================
--- trunk/packages/molphy/trunk/debian/README (rev 0)
+++ trunk/packages/molphy/trunk/debian/README 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,38 @@
+MOLPHY: A Computer Program Package for Molecular Phylogenetics
+
+Readme
+ This is the MOLPHY (ProtML) distribution, version 2.3.
+ Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
+ All rights reserved.
+
+ MOLPHY is a program package for MOLecular PHYlogenetics.
+
+ProtML is a main program in MOLPHY for inferring evolutionary trees from
+PROTein (amino acid) sequences by using the Maximum Likelihood method.
+
+Programs (C language)
+ ProtML: Maximum Likelihood Inference of Protein Phylogeny
+ NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
+ ProtST: Basic Statistics of Protein Sequences
+ NucST: Basic Statistics of Nucleic Acid Sequences
+ NJdist: Neighbor Joining Phylogeny from Distance Matrix
+Utilities (Perl)
+ mollist: get identifiers list molrev: reverse DNA sequences
+ molcat: concatenate sequences molcut: get partial sequences
+ molmerge: merge sequences nuc2ptn: DNA -> Amino acid
+ rminsdel: remove INS/DEL sites molcodon: get specified codon sites
+ molinfo: get varied sites mol2mol: MOLPHY format beautifer
+ inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved
+ mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY
+ must2mol: MUST -> MOLPHY etc.
+
+MOLPHY is a free software, and you can use and redistribute it.
+The programs are written in a standard subset of C with UNIX-like OS.
+The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS.
+MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and
+HP9000/700 (cc, c89 & gcc with HP-UX 9.05).
+However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh.
+
+NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available
+by anonymous ftp in sunmh.ism.ac.jp(133.58.12.20): /pub/molphy*
+or in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/.
Added: trunk/packages/molphy/trunk/debian/README.Debian
===================================================================
--- trunk/packages/molphy/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/molphy/trunk/debian/README.Debian 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,62 @@
+molphy for DEBIAN
+-----------------
+
+Because there are no upstream changes since 5 years I consider the
+project to be dead. Anyway it is used in Arb which I want to package
+I build this package separately. Thus I also applied all patches
+from Arb.
+
+Molphy uses a strange source philosophy. In the original Makefile
+some source files are forced to be a copy of some others. The
+different targets are just built by different defines. Because I
+had to modify the source package (it was not gzipped) I decided to
+use symlinks instead of the identical copies to represent this fact
+and to make it easier to keep patches in sync.
+
+Thos files are:
+ Source Link (*) means there was a patch in Arb
+ (???) Missing in source
+ distan.c Ndistan.c
+ dmlproc.c Ndmlproc.c (???)
+ mlklhd.c Nmlklhd.c
+ protdml.c Nucdml.c (???)
+ protml.c Nucml.c Nuctpm.c Prottpm.c (*)
+ protst.c Nucst.c
+ pstree.c Dpstree.c (*)
+ seqstat.c Nseqstat.c
+ tpmproc.c Ntpmproc.c (???)
+ tranprb.c Ntranprb.c Ntrnprbt.c Trnprbt.c
+ tridist.c Njdist.c
+
+Strangely enough there is a RMSRC rule in the Makefile which might have
+deleted the sources marked with (???). There is no rule to rebuild those
+files ...
+I removed at least those filenames from the RMSRC rule which obviousely
+are needed to build some targets to avoid an accident.
+
+The Arb patches include a header file prot_tml.h which was created using
+a tool named mkptypes with the following description:
+
+ Program to extract function declarations from C source code
+ Written by Eric R. Smith and placed in the public domain
+ Thanks to:
+ Jwahar R. Bammi, for catching several bugs and providing the Unix makefiles
+ Byron T. Jenings Jr. for cleaning up the space code, providing a Unix
+ manual page, and some ANSI and C++ improvements.
+ Skip Gilbrech for code to skip parameter names in prototypes.
+ ... and many others for helpful comments and suggestions.
+ Patchlevel 1: Feb. 16, 1991
+
+The package is shipped with a documentation of the old version 1.
+Well - better old documentation than non documentation. I found it on
+ http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/PROTMLver1.DOC
+Please write an e-mail if you know about any more recent documentation.
+
+The same URL has some Examples. Those examples had some result files
+which are built with an older version (2.2) than this one (2.3b3) which
+differ more or less from the results of this package. I ship those
+results which are more different than some floats which differ below 1%.
+Please read /usr/share/doc/molphy/examples/tests/compare/README.compare
+for further explanation. There is a makefile to test the examples.
+
+Andreas Tille <tille at debian.org> Mon, 29 Oct 2001 22:34:09 +0100
Added: trunk/packages/molphy/trunk/debian/changelog
===================================================================
--- trunk/packages/molphy/trunk/debian/changelog (rev 0)
+++ trunk/packages/molphy/trunk/debian/changelog 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,46 @@
+molphy (2.3b3-4) unstable; urgency=low
+
+ * Group maintenance according to Debian-Med group policy
+ * Do not auto generate debian/control
+ * Standards-Version: 3.7.3 (no changes needed)
+ * Moved Homepage from long description to tags
+ * Removed XB-Tag which is not used
+ * Removed [Biology] from short description
+ * Fixed typo in debian/copyright
+ * Rewritten debian/mollist.1 to avoid lintian warning about
+ bad whatis entry
+
+ -- Andreas Tille <tille at debian.org> Sun, 02 Mar 2008 21:41:40 +0100
+
+molphy (2.3b3-3) unstable; urgency=low
+
+ * Standards-Version: 3.7.2 (no changes needed)
+ * Switched to cdbs
+ * Added DebTags
+
+ -- Andreas Tille <tille at debian.org> Sun, 10 Sep 2006 15:44:10 +0200
+
+molphy (2.3b3-2) unstable; urgency=low
+
+ * Rebuild to remove /usr/doc link
+ * Standards-Version: 3.6.2.1
+ * debian/compat
+ * Mention new home page in debian/{copyright,control}
+ * debhelper (>= 4)
+ * Use -O3 instead of -O2
+
+ -- Andreas Tille <tille at debian.org> Sat, 13 Aug 2005 11:22:43 +0200
+
+molphy (2.3b3-1) unstable; urgency=low
+
+ * Initial Release.
+ closes: #118355
+ * Rebuild source tarball because it was not gzipped. Used symlinks
+ instead of copies from some source files.
+ * Applied Arb patches.
+ * Wrote manpages
+ * Added documentation of older version because MolPhy comes without
+ any documentation
+ * Added examples and makefile to test them.
+
+ -- Andreas Tille <tille at debian.org> Mon, 12 Nov 2001 10:56:06 +0100
Added: trunk/packages/molphy/trunk/debian/compat
===================================================================
--- trunk/packages/molphy/trunk/debian/compat (rev 0)
+++ trunk/packages/molphy/trunk/debian/compat 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1 @@
+5
Added: trunk/packages/molphy/trunk/debian/control
===================================================================
--- trunk/packages/molphy/trunk/debian/control (rev 0)
+++ trunk/packages/molphy/trunk/debian/control 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,33 @@
+Source: molphy
+Section: non-free/science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5)
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/molphy/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/molphy/trunk/
+Homepage: http://www.ism.ac.jp/ismlib/softother.e.html
+
+Package: molphy
+Architecture: any
+Depends: ${shlibs:Depends}, ${perl:Depends}
+Suggests: phylip
+Description: Program Package for MOLecular PHYlogenetics
+ ProtML is a main program in MOLPHY for inferring evolutionary trees from
+ PROTein (amino acid) sequences by using the Maximum Likelihood method.
+ Other programs (C language)
+ NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
+ ProtST: Basic Statistics of Protein Sequences
+ NucST: Basic Statistics of Nucleic Acid Sequences
+ NJdist: Neighbor Joining Phylogeny from Distance Matrix
+ Utilities (Perl)
+ mollist: get identifiers list molrev: reverse DNA sequences
+ molcat: concatenate sequences molcut: get partial sequences
+ molmerge: merge sequences nuc2ptn: DNA -> Amino acid
+ rminsdel: remove INS/DEL sites molcodon: get specified codon sites
+ molinfo: get varied sites mol2mol: MOLPHY format beautifer
+ inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved
+ mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY
+ must2mol: MUST -> MOLPHY etc.
Added: trunk/packages/molphy/trunk/debian/copyright
===================================================================
--- trunk/packages/molphy/trunk/debian/copyright (rev 0)
+++ trunk/packages/molphy/trunk/debian/copyright 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,23 @@
+This package was debianized by Andreas Tille <tille at debian.org>
+Mon, 5 Nov 2001 23:50:39 +0100
+
+Homepage:
+ http://www.ism.ac.jp/ismlib/softother.e.html
+
+It was downloaded by anonymous ftp from:
+ ftp://ftp.ism.ac.jp/pub/ISMLIB/MOLPHY/molphy-2.3b3.tar.Z
+
+The examples and the documentation was found on
+ http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/
+
+Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
+All rights reserved.
+
+License:
+
+MOLPHY is a free software, and you can use and redistribute it.
+
+I wrote an e-mail to the authors if they could fix this license because
+it conflicts with DFSG #3 (Derived works) but I got no response yet.
+So I just put the package under non-free and I'm hoping that someone
+will respond the next couple of weeks.
Added: trunk/packages/molphy/trunk/debian/dirs
===================================================================
--- trunk/packages/molphy/trunk/debian/dirs (rev 0)
+++ trunk/packages/molphy/trunk/debian/dirs 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/molphy/trunk/debian/docs
===================================================================
--- trunk/packages/molphy/trunk/debian/docs (rev 0)
+++ trunk/packages/molphy/trunk/debian/docs 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,3 @@
+debian/FORMAT
+debian/PROTMLver1.DOC
+debian/README
Added: trunk/packages/molphy/trunk/debian/examples
===================================================================
--- trunk/packages/molphy/trunk/debian/examples (rev 0)
+++ trunk/packages/molphy/trunk/debian/examples 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1 @@
+debian/tests
Added: trunk/packages/molphy/trunk/debian/install
===================================================================
--- trunk/packages/molphy/trunk/debian/install (rev 0)
+++ trunk/packages/molphy/trunk/debian/install 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,6 @@
+src/protml usr/bin
+src/protst usr/bin
+src/nucml usr/bin
+src/nucst usr/bin
+src/njdist usr/bin
+src/totalml usr/bin
Added: trunk/packages/molphy/trunk/debian/links
===================================================================
--- trunk/packages/molphy/trunk/debian/links (rev 0)
+++ trunk/packages/molphy/trunk/debian/links 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,47 @@
+usr/share/man/man1/protml.1 usr/share/man/man1/njdist.1
+usr/share/man/man1/protml.1 usr/share/man/man1/nucml.1
+usr/share/man/man1/protml.1 usr/share/man/man1/nucst.1
+usr/share/man/man1/protml.1 usr/share/man/man1/protst.1
+usr/share/man/man1/protml.1 usr/share/man/man1/totalml.1
+
+usr/share/man/man1/mollist.1 usr/share/man/man1/ali2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/clus2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/degene4l.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/degene4.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/disjoint.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/dna2ami.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/eali2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/egetcds.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/getcds.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/ggetcds.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/inf2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/infocode2.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/infocode.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/int2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mc2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mega2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mol2inf.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mol2int.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mol2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mol2phy.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/mol2seq.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molcat.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molcodon.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molcons.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molcut.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molinfo.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molmerge.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molrev.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/molsplit.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/must2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/njt2tpl.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/nuc2code.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/nuc2NUC.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/nuc2ptn.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/phy2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/rmid3.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/rminsdel.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/rmleu.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/rmsyno.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/seq2mol.1
+usr/share/man/man1/mollist.1 usr/share/man/man1/seqwrap.1
Added: trunk/packages/molphy/trunk/debian/manpages
===================================================================
--- trunk/packages/molphy/trunk/debian/manpages (rev 0)
+++ trunk/packages/molphy/trunk/debian/manpages 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,2 @@
+debian/mollist.1
+debian/protml.1
Added: trunk/packages/molphy/trunk/debian/mollist.1
===================================================================
--- trunk/packages/molphy/trunk/debian/mollist.1 (rev 0)
+++ trunk/packages/molphy/trunk/debian/mollist.1 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,214 @@
+'\" t
+.\" ** The above line should force tbl to be a preprocessor **
+.\" Copyright (C), 2001, Andreas Tille <tille at debian.org>
+.\"
+.\" You may distribute under the terms of the GNU General Public
+.\" License as specified in the file COPYING that comes with the
+.\" man_db distribution.
+.\"
+.\"
+.TH "MolPhy Utilities" 1 "November 7, 2001" "MOLecular PHYlogenetics"
+.SH NAME
+.B mollist
+\- get identifiers list
+.br
+.B molrev
+\- reverse DNA sequences
+.br
+.B molcat
+\- concatenate sequences
+.br
+.B molcut
+\- get partial sequences
+.br
+.B molmerge
+\- merge sequences
+.br
+.B nuc2ptn
+\- DNA -> Amino acid
+.br
+.B rminsdel
+\- remove INS/DEL sites
+.br
+.B molcodon
+\- get specified codon sites
+.br
+.B molinfo
+\- get varied sites
+.br
+.B mol2mol
+\- MOLPHY format beautifer
+.br
+.B int2mol
+\- Interleaved -> MOLPHY
+.br
+.B mol2int
+\- MOLPHY -> Interleaved
+.br
+.B mol2phy
+\- MOLPHY -> Sequential
+.br
+.B phy2mol
+\- Sequential -> MOLPHY
+.br
+.B must2mol
+\- MUST -> MOLPHY
+.br
+many more perl conversion utilities which are not further described
+
+.SH SYNOPSIS
+MolPhy Utilities is a program package for MOLecular PHYlogenetics
+which includes several Perl utilities:
+
+
+.B mollist
+.RB [sequence_file]
+.br
+.B molrev
+.RB [sequence_file]
+.br
+.B molcat
+.RB [sequence_file]
+.br
+.B molcut
+.RB [sequence_file]
+.br
+.B molmerge
+.RB [sequence_file]
+.br
+.B nuc2ptn
+.RB [switches]
+.RB [sequence_file]
+.br
+.B rminsdel
+.RB [switches]
+.RB [sequence_file]
+.br
+.B molcodon
+.RB [sequence_file]
+.br
+.B molinfo
+.RB [switches]
+.RB [sequence_file]
+.br
+.B mol2mol
+.RB [sequence_file]
+.br
+.B inl2mol
+.RB [sequence_file]
+.br
+.B mol2int
+.RB [sequence_file]
+.br
+.B mol2phy
+.RB [sequence_file]
+.br
+.B phy2mol
+.RB [sequence_file]
+.br
+.B must2mol
+.RB [sequence_file]
+.br
+.B ali2mol
+.RB [sequence_file]
+.br
+.B clus2mol
+.RB [sequence_file]
+.br
+.B degene4l
+.RB [switches]
+.RB [sequence_file]
+.br
+.B degene4
+.RB [switches]
+.RB [sequence_file]
+.br
+.B disjoint
+.RB [sequence_file]
+.br
+.B dna2ami
+.RB [options]
+.RB [no_align_files]
+.br
+.B eali2mol
+.RB [EMBL_ALIGN_file]
+.br
+.B egetcds
+.RB [EMBL_file]
+.br
+.B getcds
+.RB [EMBL_file]
+.br
+.B egetcds
+.RB [Genbank_file]
+.br
+.B info2mol
+.RB [sequence_file]
+.br
+.B infocode
+.RB [switches]
+.RB [sequence_file]
+.br
+.B infocode
+.RB [switches]
+.RB [sequence_file]
+.br
+.B mc2mol
+.RB [sequence_file]
+.br
+.B mega2mol
+.RB [sequence_file]
+.br
+.B mol2info
+.RB [sequence_file]
+.br
+.B mol2seq
+.RB [sequence_file]
+.br
+.B molcons
+.RB [sequence_file]
+.br
+.B molsplit
+.RB [sequence_file]
+.br
+.B njt2tpl
+.RB [machine_readable_tree_with_branch_length]
+.br
+.B mol2mol
+.RB [sequence_file]
+.br
+.B nuc2NUC
+.RB [sequence_file]
+.br
+.B rmid3
+.RB [switches]
+.RB [sequence_file]
+.br
+.B rmleu
+.RB [switches]
+.RB [sequence_file]
+.br
+.B rmsyno
+.RB [switches]
+.RB [sequence_file]
+.br
+.B seq2mol
+.RB [sequence_file]
+.br
+.B seqwrap
+.RB [file]
+
+.SH DESCRIPTION
+This is the Debian GNU/Linux version of the
+MOLPHY (ProtML) distribution, version 2.3.
+Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
+All rights reserved.
+
+MOLPHY is a program package for MOLecular PHYlogenetics.
+
+The perl utilities above are usefull to convert different formats
+of phylogenetic data.
+
+.SH AUTHOR
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/molphy/trunk/debian/patches/src.diff
===================================================================
--- trunk/packages/molphy/trunk/debian/patches/src.diff (rev 0)
+++ trunk/packages/molphy/trunk/debian/patches/src.diff 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,667 @@
+diff -urbN src.orig/getseq.c src/getseq.c
+--- src.orig/getseq.c 1996-07-02 16:56:00.000000000 +0200
++++ src/getseq.c 2006-09-10 16:19:56.000000000 +0200
+@@ -4,7 +4,7 @@
+ */
+
+ #include "protml.h"
+-
++#include "prot_tml.h"
+
+ void
+ getsize(ifp, maxspc, numsite, commentp)
+@@ -18,7 +18,7 @@
+
+ if (fgets(line, BUFLINE, ifp) != NULL) {
+ if (sscanf(line, "%d %d", maxspc, numsite) == 2) {
+- for (cp = line; isdigit(*cp) || isspace(*cp) && *cp != '\0'; cp++)
++ for (cp = line; isdigit(*cp) || isspace(*cp) /*&& *cp != '\0'*/; cp++)
+ ;
+ *commentp = new_cvector(strlen(cp) + 1);
+ if (*cp != '\0') {
+diff -urbN src.orig/Makefile src/Makefile
+--- src.orig/Makefile 1996-07-02 16:56:36.000000000 +0200
++++ src/Makefile 2006-09-10 16:19:56.000000000 +0200
+@@ -1,10 +1,13 @@
+-INSTALLDIR = ./.. # /usr/local/bin/molphy
++.SUFFIXES: .o .c
++
++INSTALLDIR = /usr/local/bin/molphy
+
+ CC = gcc # cc, gcc, c89
+-CFLAGS = -O # -O4 or +O
++CFLAGS = -O3 # -O4 or +O
+ DEFINE = #
+-LIBS = -lm # -lM
+-CP = cp # copy command
++LIBS = -lm -lc
++# CP = cp -a
++CP = ln -s
+ NUCLE = -DNUC
+ NJLE = -DNJ
+ SDLE = -DSD
+@@ -82,102 +85,102 @@
+
+ # protml nucml
+
+-protml.o : protml.c protml.h molphy.h
++protml.o : protml.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c protml.c
+ Nucml.c : protml.c optimtpm.c abratio.c
+ $(CP) protml.c Nucml.c
+-Nucml.o : Nucml.c protml.h molphy.h optimtpm.c abratio.c
++Nucml.o : Nucml.c protml.h molphy.h optimtpm.c abratio.c matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nucml.c
+-getseq.o : getseq.c protml.h molphy.h
++getseq.o : getseq.c protml.h molphy.h prot_tml.h
+ $(CC) $(CFLAGS) $(DEFINE) -c getseq.c
+-seqproc.o : seqproc.c protml.h molphy.h
++seqproc.o : seqproc.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c seqproc.c
+-tranprb.o : tranprb.c protml.h molphy.h
++tranprb.o : tranprb.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c tranprb.c
+ Ntranprb.c : tranprb.c
+ $(CP) tranprb.c Ntranprb.c
+-Ntranprb.o : Ntranprb.c protml.h molphy.h
++Ntranprb.o : Ntranprb.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Ntranprb.c
+-distan.o : distan.c protml.h molphy.h
++distan.o : distan.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c distan.c
+ Ndistan.c : distan.c
+ $(CP) distan.c Ndistan.c
+-Ndistan.o : Ndistan.c protml.h molphy.h
++Ndistan.o : Ndistan.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Ndistan.c
+-mltree.o : mltree.c protml.h molphy.h
++mltree.o : mltree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mltree.c
+-altree.o : altree.c protml.h molphy.h
++altree.o : altree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c altree.c
+-qltree.o : qltree.c protml.h molphy.h
++qltree.o : qltree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c qltree.c
+-sltree.o : sltree.c protml.h molphy.h
++sltree.o : sltree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c sltree.c
+-njtree.o : njtree.c protml.h molphy.h
++njtree.o : njtree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c njtree.c
+-njmtree.o : njmtree.c protml.h molphy.h
++njmtree.o : njmtree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c njmtree.c
+-mlklhd.o : mlklhd.c protml.h molphy.h
++mlklhd.o : mlklhd.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mlklhd.c
+ Nmlklhd.c : mlklhd.c
+ $(CP) mlklhd.c Nmlklhd.c
+-Nmlklhd.o : Nmlklhd.c protml.h molphy.h
++Nmlklhd.o : Nmlklhd.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nmlklhd.c
+-prtree.o : prtree.c protml.h molphy.h
++prtree.o : prtree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c prtree.c
+-pstree.o : pstree.c protml.h molphy.h
++pstree.o : pstree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c pstree.c
+
+-protproc.o : protproc.c protml.h molphy.h
++protproc.o : protproc.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c protproc.c
+-nucproc.o : nucproc.c protml.h molphy.h
++nucproc.o : nucproc.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c nucproc.c
+-dyhfjtt.o : dyhfjtt.c protml.h molphy.h
++dyhfjtt.o : dyhfjtt.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c dyhfjtt.c
+-mtrev24.o : mtrev24.c protml.h molphy.h
++mtrev24.o : mtrev24.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mtrev24.c
+
+ # protst nucst
+
+-protst.o : protst.c protst.h molphy.h
++protst.o : protst.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c protst.c
+ Nucst.c : protst.c
+ $(CP) protst.c Nucst.c
+-Nucst.o : Nucst.c protst.h molphy.h
++Nucst.o : Nucst.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nucst.c
+
+-seqstat.o : seqstat.c protst.h molphy.h
++seqstat.o : seqstat.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c seqstat.c
+ Nseqstat.c : seqstat.c
+ $(CP) seqstat.c Nseqstat.c
+-Nseqstat.o : Nseqstat.c protst.h molphy.h
++Nseqstat.o : Nseqstat.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nseqstat.c
+
+ # tridist njdist
+
+-tridist.o : tridist.c tridist.h molphy.h
++tridist.o : tridist.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c tridist.c
+-triproc.o : triproc.c tridist.h molphy.h
++triproc.o : triproc.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c triproc.c
+ Njdist.c : tridist.c
+ $(CP) tridist.c Njdist.c
+-Njdist.o : Njdist.c tridist.h molphy.h
++Njdist.o : Njdist.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) $(NJLE) -c Njdist.c
+-njproc.o : njproc.c tridist.h molphy.h
++njproc.o : njproc.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c njproc.c
+ sddist.o : sddist.c sddist.h molphy.h
+ $(CC) $(CFLAGS) $(DEFINE) $(SDLE) -c sddist.c
+ sdproc.o : sdproc.c sddist.h molphy.h
+ $(CC) $(CFLAGS) $(DEFINE) -c sdproc.c
+-distproc.o : distproc.c tridist.h molphy.h
++distproc.o : distproc.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c distproc.c
+ Dpstree.c : pstree.c
+ $(CP) pstree.c Dpstree.c
+-Dpstree.o : Dpstree.c tridist.h molphy.h
++Dpstree.o : Dpstree.c tridist.h molphy.h protml.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) $(NJLE) -c Dpstree.c
+
+ # totalml
+
+-totalml.o : totalml.c totalml.h molphy.h
++totalml.o : totalml.c totalml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c totalml.c
+
+ # tmlprot
+@@ -192,11 +195,11 @@
+
+ Prottpm.c : protml.c
+ $(CP) protml.c Prottpm.c
+-Prottpm.o : Prottpm.c protml.h molphy.h
++Prottpm.o : Prottpm.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) -DTPM $(DEFINE) -c Prottpm.c
+ Nuctpm.c : protml.c
+ $(CP) protml.c Nuctpm.c
+-Nuctpm.o : Nuctpm.c protml.h molphy.h
++Nuctpm.o : Nuctpm.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) -DTPM $(NUCLE) $(DEFINE) -c Nuctpm.c
+
+ tpmproc.o : tpmproc.c protml.h molphy.h
+@@ -234,11 +237,12 @@
+
+ matrixut.o : matrixut.c matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c matrixut.c
+-mygetopt.o : mygetopt.c
++mygetopt.o : mygetopt.c molphy.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mygetopt.c
+
+ install : $(PRGS)
+- $(CP) $(PRGS) $(INSTALLDIR)
++ mkdir -p $(INSTALLDIR)
++ cp -a $(PRGS) $(INSTALLDIR)
+ cd $(INSTALLDIR); \
+ chmod 755 $(PRGS)
+
+@@ -272,6 +276,15 @@
+ rcp [a-z]*.c *.h Makefile sunmh:/home/sunmh/adachi/work/molphybeta
+
+ RMSRC :
+- rm bdate.c compcrit.c dmlproc.c protdml.c protdml.h ptnlkl.c \
+- sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c tpmproc.c \
++# rm bdate.c compcrit.c protdml.h ptnlkl.c \
++# sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c \
++# triadml.c
++ @echo This target intends to remove the following files
++ @echo bdate.c compcrit.c protdml.h ptnlkl.c \
++ sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c \
+ triadml.c
++ @echo This is prevented because I consider it to be a bad idea to remove sources.
++
++## The following file is unused in original molphy and there are just plain
++## dependencies in the arb pachage because it was automatically generated
++## mtrev22.o: protml.h molphy.h matrixut.h
+diff -urbN src.orig/molphy.h src/molphy.h
+--- src.orig/molphy.h 1996-07-02 16:56:01.000000000 +0200
++++ src/molphy.h 2006-09-10 16:19:56.000000000 +0200
+@@ -17,7 +17,7 @@
+ #define DIR_CHAR '/' /* directory separator '/' (UNIX) */
+ #else
+ #define SW_CHAR '/' /* switch charcter '/' (MSDOS) */
+-#define DIR_CHAR '\' /* directory separator '\' (MSDOS) */
++#define DIR_CHAR '\\' /* directory separator '\' (MSDOS) */
+ #endif
+
+ #ifdef RAND_MAX
+diff -urbN src.orig/nucproc.c src/nucproc.c
+--- src.orig/nucproc.c 1996-07-02 16:56:00.000000000 +0200
++++ src/nucproc.c 2006-09-10 16:19:56.000000000 +0200
+@@ -20,9 +20,7 @@
+ };
+
+
+-int
+-isacid(c)
+-char c;
++int isacid(char c)
+ {
+ /* nuc */
+ switch (c) {
+diff -urbN src.orig/protml.c src/protml.c
+--- src.orig/protml.c 1996-07-02 16:56:00.000000000 +0200
++++ src/protml.c 2006-09-10 16:36:01.000000000 +0200
+@@ -1124,6 +1124,7 @@
+ prtopology(Ctree);
+ resulttree(Ctree);
+ pstree(Epsfp, Ctree);
++ fputcphylogeny(Trefp, Ctree);
+ FREE_LPMATRIX(Lklptrn);
+
+ } else if (Njoin_optn) { /* NJ MODE */
+diff -urbN src.orig/protst.c src/protst.c
+--- src.orig/protst.c 1996-07-02 16:56:00.000000000 +0200
++++ src/protst.c 2006-09-10 16:19:56.000000000 +0200
+@@ -136,31 +136,31 @@
+ }
+
+
+-#if 0
+-void
+-header(ofp, maxspc, numsite, commentp)
+-FILE *ofp;
+-int *maxspc;
+-int *numsite;
+-char **commentp;
+-{
+- time_t ct;
+- char *datetime, *ip, *jp;
+-
+- fprintf(ofp, "%s %s ", Prog_name, VERSION);
+-
+- ct = time(NULL);
+- datetime = ctime(&ct);
+- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++;
+- *ip = '\0';
+- fputs(datetime + 4, ofp);
+- fputs(" ", ofp);
+- fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp);
+- free_cvector(*commentp);
+-} /*_ header */
+-#endif
++/* #if 0 */
++/* void */
++/* header(ofp, maxspc, numsite, commentp) */
++/* FILE *ofp; */
++/* int *maxspc; */
++/* int *numsite; */
++/* char **commentp; */
++/* { */
++/* time_t ct; */
++/* char *datetime, *ip, *jp; */
++
++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */
++
++/* ct = time(NULL); */
++/* datetime = ctime(&ct); */
++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */
++/* *ip = '\0'; */
++/* fputs(datetime + 4, ofp); */
++/* fputs(" ", ofp); */
++/* fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp); */
++/* free_cvector(*commentp); */
++/* } / *_ header * / */
++/* #endif */
+
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
+diff -urbN src.orig/prot_tml.h src/prot_tml.h
+--- src.orig/prot_tml.h 1970-01-01 01:00:00.000000000 +0100
++++ src/prot_tml.h 2006-09-10 16:19:56.000000000 +0200
+@@ -0,0 +1,241 @@
++#ifndef P_
++# if defined(__STDC__) || defined(__cplusplus)
++# define P_(s) s
++# else
++# define P_(s) ()
++# endif
++#else
++# error P_ already defined elsewhere
++#endif
++
++
++/* getseq.c */
++void getsize P_((FILE *ifp, int *maxspc, int *numsite, char **commentp));
++void getid P_((FILE *ifp, char **identif, char **sciname, char **engname, int *nl, int *notu));
++void getsites P_((FILE *ifp, cmatrix seqchar, int numsite, int *nl, int *notu));
++void getseq P_((FILE *ifp, char **identif, char **sciname, char **engname, cmatrix seqchar, int maxspc, int numsite));
++void getidsites P_((FILE *ifp, cmatrix identif, cmatrix seqchar, int numsite, int *nl, int *notu));
++void getseqs P_((FILE *ifp, char **identif, cmatrix seqchar, int maxspc, int numsite));
++void getseqi P_((FILE *ifp, char **identif, cmatrix seqchar, int maxspc, int numsite));
++void fputid P_((FILE *ofp, char *name, int maxcolumn));
++void prsequence P_((FILE *ofp, char **identif, char **seqchar, int maxspc, int maxsite));
++
++/* seqproc.c */
++void convseq P_((imatrix seqconint, int maxspc, int numptrn));
++void getfreqepm P_((cmatrix seqchar, double *freqemp, int maxspc, int maxsite));
++void convfreq P_((double *freqemp));
++void radixsort P_((cmatrix seqchar, ivector alias, int maxspc, int maxsite, int *numptrn));
++void condenceseq P_((cmatrix seqchar, ivector alias, imatrix seqconint, ivector weight, int maxspc, int maxsite, int numptrn));
++void getnumsites P_((imatrix seqconint, ivector numsites, ivector weight, int numspc, int numptrn));
++void prcondenceseq P_((char **identif, imatrix seqconint, ivector weight, int numspc, int numsite, int numptrn));
++
++/* mltree.c */
++Node **new_npvector P_((int n));
++void free_npvector P_((Node **v));
++Tree *new_tree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++int getbuftree P_((int numspc, cmatrix identif));
++void changedistan P_((dmatrix distanmat, dvector distanvec, int numspc));
++void getproportion P_((double *proportion, dvector distanvec, int maxpair));
++Infotree *newinfotrees P_((int numtree, int buftree));
++Infoaltree *newinfoaltrees P_((int numaltree, int buftree));
++void getnumtree P_((FILE *ifp, int *numtree));
++void getusertree P_((FILE *ifp, cvector strtree, int buftree));
++Node *internalnode P_((Tree *tr, char **cpp, int *ninode, char *st));
++void constructtree P_((Tree *tr, cvector strtree));
++void prcurtree P_((Tree *tr));
++void pathing P_((Tree *tr));
++void lslength P_((Tree *tr, dvector distanvec, int numspc));
++void slslength P_((Tree *tr, dmatrix dmat, int ns));
++void fmlength P_((Tree *tr, dmatrix dmat, int ns));
++void resulttree P_((Tree *tr));
++void bootstrap P_((Infotree *infotrs, LPMATRIX lklptrn));
++void tabletree P_((Infotree *infotrs, LPMATRIX lklptrn));
++void tableinfo P_((Infotree *infotrs));
++void rerootq P_((Tree *tr, int numspc));
++void outlklhd P_((LPMATRIX lklptrn));
++void putsortseq P_((Tree *tr));
++
++/* altree.c */
++Tree *new_atree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++Node *new_dnode P_((void));
++Node *new_anode P_((void));
++Node ***new_nodematrix P_((int nrow, int ncol));
++void free_nodematrix P_((Node ***m));
++void aproxlkl P_((Tree *tr));
++void aproxlkl P_((Tree *tr));
++void praproxlkl P_((Tree *tr));
++void aproxtree P_((Tree *tr, int ntr));
++void wedge P_((Tree *tr, int onode, Node **poolnode, Node **addposition, ivector poolorder, Node *op));
++void autoconstruction P_((Tree *tr, int onode, Node **poolnode, Node **addposition, ivector poolorder));
++Node *inbranode P_((Tree *tr, char **cpp, int *nenode, int numorder, Node ***poolnode2, cvector st));
++void streeinit P_((Tree *tr, cvector strtree, Node **poolnode, Node **addposition, ivector poolorder));
++void atreeinit P_((Tree *tr, Node **poolnode, Node **addposition, ivector poolorder));
++void tablealtree P_((int nt));
++
++/* qltree.c */
++Infoqltree *newinfoqltrees P_((int n, int maxbrnch));
++Infoaddtree *newinfoaddtree P_((int buftree));
++void initturn P_((Tree *tr));
++void randturn P_((Tree *tr));
++void convertdistan P_((Tree *tr, int numspc, dmatrix distanmat, dvector distanvec));
++void praproxlkl2 P_((FILE *fp, Tree *tr));
++int addotu P_((Tree *tr, Node *cp, Node *np, Node *ip, int cnspc));
++int addotual P_((Tree *tr, Node *cp, Node *np, Node *ip, dvector lengs));
++void roundtree P_((Tree *tr, int cnspc, Infoqltree *infoqltrees, Infoqltree *qhead, Infoqltree *qtail));
++void qtreeinit P_((Tree *tr));
++void tableaddtree P_((Infoaddtree *head, int numaddtree));
++
++/* sltree.c */
++Tree *new_stree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++Infosltree *newinfosltrees P_((int num, int maxbrnch));
++void insertbranch P_((Node *ibp, Node *np));
++void deletebranch P_((Node *ibp, Node *np));
++void movebranch P_((Node *jbp, Node *ip));
++void removebranch P_((Node *jbp, Node *ip));
++void subpathing P_((Node *np));
++void copylength P_((Tree *tr, dvector lengs));
++Node *sdml P_((Tree *tr, Node *op));
++void decomposition P_((Tree *tr, int n, Infosltree *infosltrees));
++void stardecomp P_((Tree *tr, int maxibrnch));
++dcube new_dcubesym P_((int nrow, int ncol));
++void free_dcubesym P_((dcube c));
++void ystardecomp P_((Tree *tr));
++void xstardecomp P_((Tree *tr));
++
++/* njtree.c */
++Tree *new_njtree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++void free_njtree P_((Tree *tr, int maxspc, int maxibrnch));
++double emledis P_((double dis, Node *ip, Node *kp));
++double imledis P_((double dis, Node *ip, Node *kp));
++void redmat P_((dmatrix dmat, double dij, Node **psotu, ivector otu, int restsp, int ii, int jj, int ns));
++void enjtree P_((Tree *tr, dmatrix distan, int ns, boolean flag));
++
++/* njmtree.c */
++void initsubplkl P_((Node *op));
++void mlepartlen P_((Node *ip, Node *jp, Node **rotup, int nr, int ns));
++void remldmat P_((dmatrix dmat, double dij, Node **psotu, Node **rotup, int otui, int otuj, int ns));
++void njmtree P_((Tree *tr, dmatrix distan, int ns, boolean flag));
++
++/* prtree.c */
++void putctopology P_((Tree *tr));
++void fputctopology P_((FILE *fp, Tree *tr));
++void fputcphylogeny P_((FILE *fp, Tree *tr));
++void prtopology P_((Tree *tr));
++void strctree P_((Tree *tr, char *ltree));
++
++/* pstree.c */
++void psdicter P_((FILE *fp));
++void pstree P_((FILE *fp, Tree *tr));
++
++/* matrixut.c */
++void maerror P_((char *message));
++fvector new_fvector P_((int n));
++fmatrix new_fmatrix P_((int nrow, int ncol));
++fcube new_fcube P_((int ntri, int nrow, int ncol));
++void free_fvector P_((fvector v));
++void free_fmatrix P_((fmatrix m));
++void free_fcube P_((fcube c));
++dvector new_dvector P_((int n));
++dmatrix new_dmatrix P_((int nrow, int ncol));
++dcube new_dcube P_((int ntri, int nrow, int ncol));
++void free_dvector P_((dvector v));
++void free_dmatrix P_((dmatrix m));
++void free_dcube P_((dcube c));
++cvector new_cvector P_((int n));
++cmatrix new_cmatrix P_((int nrow, int ncol));
++ccube new_ccube P_((int ntri, int nrow, int ncol));
++void free_cvector P_((cvector v));
++void free_cmatrix P_((cmatrix m));
++void free_ccube P_((ccube c));
++ivector new_ivector P_((int n));
++imatrix new_imatrix P_((int nrow, int ncol));
++icube new_icube P_((int ntri, int nrow, int ncol));
++void free_ivector P_((ivector v));
++void free_imatrix P_((imatrix m));
++void free_icube P_((icube c));
++
++/* mygetopt.c */
++int mygetopt P_((int argc, char **argv, char *optstring));
++
++/* protml.c */
++void copyright P_((void));
++void usage P_((void));
++void helpinfo P_((void));
++int main P_((int argc, char **argv));
++void header P_((FILE *ofp, int *maxspc, int *numsite, char **commentp));
++void headerd P_((FILE *ofp, int *maxspc, int *numsite, char **commentp));
++void pml P_((FILE *ifp, FILE *ofp));
++
++/* protproc.c */
++int isacid P_((int c));
++int acid2int P_((int c));
++char acid2chint P_((int c));
++char chint2acid P_((int c));
++char int2acid P_((int i));
++
++/* dyhfjtt.c */
++void dyhfjtt P_((dmattpmty r, double *f, boolean flag));
++
++/* mtrev24.c */
++void mtrev P_((dmattpmty r, double *f));
++
++/* tranprb.c */
++void elmhes P_((dmattpmty a, int *ordr, int n));
++void eltran P_((dmattpmty a, dmattpmty zz, int *ordr, int n));
++void hqr2 P_((int n, int low, int hgh, int *err, dmattpmty h, dmattpmty zz, double *wr, double *wi));
++void readrsrf P_((dmattpmty r, dvectpmty f, int n));
++void tpmonepam P_((dmattpmty a, double *f));
++void luinverse P_((dmattpmty omtrx, dmattpmty imtrx, int size));
++void mproduct P_((dmattpmty am, dmattpmty bm, dmattpmty cm, int na, int nb, int nc));
++void preigen P_((void));
++void checkevector P_((dmattpmty imtrx, int nn));
++void getrsr P_((dmattpmty a, dvectpmty ftpm));
++void tranprobmat P_((void));
++void varitpm P_((void));
++void prfreq P_((void));
++void tprobmtrx P_((double arc, dmattpmty tpr));
++void tprobmtrxt P_((double arc, dmattpmty tpr));
++void tdiffmtrx P_((double arc, dmattpmty tpr, dmattpmty td1, dmattpmty td2));
++void tprobmtrx2 P_((double arc, dmattpmty tpr));
++void tdiffmtrx2 P_((double arc, dmattpmty tpr, dmattpmty td1, dmattpmty td2));
++
++/* distan.c */
++void distance P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite));
++void lddistance P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite));
++void tdistan P_((ivector seqi, ivector seqj, dmatrix probk, ivector weight, int nptrn, double *len, double *lvari, dcube triprob));
++void tdistan2 P_((ivector seqi, ivector seqj, ivector seqk, ivector seqw, int nsite, double *len, double *lvari, dcube triprob));
++void tridistance P_((dmatrix distanmat, imatrix seqconint, ivector weight, int maxspc, int numptrn));
++void tridistance2 P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite));
++void putdistance P_((cmatrix identif, cmatrix sciname, cmatrix engname, dmatrix distanmat, int maxspc));
++void checkseq P_((imatrix seqconint, int maxspc, int numptrn));
++
++/* mlklhd.c */
++double probnormal P_((double z));
++double uprobnormal P_((double z));
++void copypart1 P_((Node *op, Node *cp));
++void prodpart1 P_((Node *op, Node *cp));
++void prodpart P_((Node *op));
++void partilkl P_((Node *op));
++void partelkl P_((Node *op));
++void partelkl2 P_((Node *op));
++void initpartlkl P_((Tree *tr));
++void regupartlkl P_((Tree *tr));
++void mlibranch P_((Node *op, double eps, int nloop));
++void mlebranch P_((Node *op, double eps, int nloop));
++void mlebranch2 P_((Node *op, double eps, int nloop));
++void evallkl P_((Node *op));
++Node *mlikelihood P_((Tree *tr));
++void ribranch P_((Node *op));
++Node *relibranch P_((Node *op));
++void mlvalue P_((Tree *tr, Infotree *infotrs));
++void reroot P_((Tree *tr, Node *rp));
++void sorttree P_((Tree *tr, Node *rp));
++void chroot P_((Tree *tr, int s1, int s2));
++void noexch P_((Node *rp, ivector exchstate));
++void reliml P_((Tree *tr, Node *op, double lklorg, LPVECTOR mlklptrn, double *rel));
++void localbp P_((dmatrix reliprob, LPVECTOR mlklptrn, LPCUBE rlklptrn, ivector whichml, int nb, int ns));
++void reliabranch P_((Tree *tr));
++void annealing P_((Tree *tr));
++void qlrsearch P_((Tree *tr));
++
++#undef P_
+diff -urbN src.orig/pstree.c src/pstree.c
+--- src.orig/pstree.c 1996-07-02 16:56:00.000000000 +0200
++++ src/pstree.c 2006-09-10 16:19:56.000000000 +0200
+@@ -153,10 +153,10 @@
+ if (len == 0) len = 1;
+ if (cp->descen) x += len;
+ if (cp->isop == NULL) { /* external node */
+- (Sciname[cp->num][0] != '\0') ?
++ (Sciname[cp->num] && Sciname[cp->num][0] != '\0') ? /* @@@OLIVER */
+ (name = Sciname[cp->num]) : (name = Identif[cp->num]);
+ s = (int)(fontw * (strlen(name) + 1) + 10);
+- if (Engname[cp->num][0] != '\0') {
++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */
+ s += (int)(fontw * (strlen(Engname[cp->num]) + 1));
+ }
+ xs = x + s;
+@@ -232,12 +232,12 @@
+ fprintf(fp, "n %3d %3d m %3d %3d l s ", x - len, y, x, y);
+ fprintf(fp, " %3d %3d m", x + (int)fontw, y-fontc);
+ fprintf(fp, " %% %3d\n", cp->num+1);
+- if (Sciname[cp->num][0] == '\0') {
++ if (Sciname[cp->num]== 0 || Sciname[cp->num][0] == '\0') { /* @@@OLIVER */
+ fprintf(fp, " Fid ff %d sf (%s) sh", fonts, Identif[cp->num]);
+ } else {
+ fprintf(fp, " Fsc ff %d sf (%s) sh", fonts, Sciname[cp->num]);
+ }
+- if (Engname[cp->num][0] != '\0') {
++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */
+ fprintf(fp, " Fid ff %d sf ( %s) sh\n",fonts,Engname[cp->num]);
+ } else {
+ fprintf(fp, "\n");
+diff -urbN src.orig/qltree.c src/qltree.c
+--- src.orig/qltree.c 1996-07-02 16:56:00.000000000 +0200
++++ src/qltree.c 2006-09-10 16:19:56.000000000 +0200
+@@ -140,7 +140,7 @@
+ } /*_ praproxlkl2 */
+
+
+-addotu(tr, cp, np, ip, cnspc)
++int addotu(tr, cp, np, ip, cnspc)
+ Tree *tr;
+ Node *cp, *np, *ip;
+ int cnspc;
+diff -urbN src.orig/totalml.c src/totalml.c
+--- src.orig/totalml.c 1996-07-02 16:56:00.000000000 +0200
++++ src/totalml.c 2006-09-10 16:19:56.000000000 +0200
+@@ -40,31 +40,31 @@
+ }
+
+
+-#if 0
+-void
+-header(ofp, numseqs, allsite, commentp)
+-FILE *ofp;
+-int *numseqs;
+-int *allsite;
+-char **commentp;
+-{
+- time_t ct;
+- char *datetime, *ip, *jp;
++/* #if 0 */
++/* void */
++/* header(ofp, numseqs, allsite, commentp) */
++/* FILE *ofp; */
++/* int *numseqs; */
++/* int *allsite; */
++/* char **commentp; */
++/* { */
++/* time_t ct; */
++/* char *datetime, *ip, *jp; */
++
++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */
++
++/* ct = time(NULL); */
++/* datetime = ctime(&ct); */
++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */
++/* *ip = '\0'; */
++/* fputs(datetime + 4, ofp); */
++/* fprintf(ofp, " %d data %d sites.\n", *numseqs, *allsite); */
++/* / * fprintf(ofp, " %d data %d sites. %s\n", *numseqs, *allsite, *commentp); * / */
++/* } / *_ header * / */
++/* #endif */
+
+- fprintf(ofp, "%s %s ", Prog_name, VERSION);
+
+- ct = time(NULL);
+- datetime = ctime(&ct);
+- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++;
+- *ip = '\0';
+- fputs(datetime + 4, ofp);
+- fprintf(ofp, " %d data %d sites.\n", *numseqs, *allsite);
+-/* fprintf(ofp, " %d data %d sites. %s\n", *numseqs, *allsite, *commentp); */
+-} /*_ header */
+-#endif
+-
+-
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
Added: trunk/packages/molphy/trunk/debian/patches/src.diff_schnurps
===================================================================
--- trunk/packages/molphy/trunk/debian/patches/src.diff_schnurps (rev 0)
+++ trunk/packages/molphy/trunk/debian/patches/src.diff_schnurps 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,806 @@
+diff -ubrN src.orig/Dpstree.c src/Dpstree.c
+--- src.orig/Dpstree.c 1996-07-02 16:56:00.000000000 +0200
++++ src/Dpstree.c 2006-09-10 15:20:27.000000000 +0200
+@@ -153,10 +153,10 @@
+ if (len == 0) len = 1;
+ if (cp->descen) x += len;
+ if (cp->isop == NULL) { /* external node */
+- (Sciname[cp->num][0] != '\0') ?
++ (Sciname[cp->num] && Sciname[cp->num][0] != '\0') ? /* @@@OLIVER */
+ (name = Sciname[cp->num]) : (name = Identif[cp->num]);
+ s = (int)(fontw * (strlen(name) + 1) + 10);
+- if (Engname[cp->num][0] != '\0') {
++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */
+ s += (int)(fontw * (strlen(Engname[cp->num]) + 1));
+ }
+ xs = x + s;
+@@ -232,12 +232,12 @@
+ fprintf(fp, "n %3d %3d m %3d %3d l s ", x - len, y, x, y);
+ fprintf(fp, " %3d %3d m", x + (int)fontw, y-fontc);
+ fprintf(fp, " %% %3d\n", cp->num+1);
+- if (Sciname[cp->num][0] == '\0') {
++ if (Sciname[cp->num]== 0 || Sciname[cp->num][0] == '\0') { /* @@@OLIVER */
+ fprintf(fp, " Fid ff %d sf (%s) sh", fonts, Identif[cp->num]);
+ } else {
+ fprintf(fp, " Fsc ff %d sf (%s) sh", fonts, Sciname[cp->num]);
+ }
+- if (Engname[cp->num][0] != '\0') {
++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */
+ fprintf(fp, " Fid ff %d sf ( %s) sh\n",fonts,Engname[cp->num]);
+ } else {
+ fprintf(fp, "\n");
+diff -ubrN src.orig/getseq.c src/getseq.c
+--- src.orig/getseq.c 1996-07-02 16:56:00.000000000 +0200
++++ src/getseq.c 2006-09-10 15:20:27.000000000 +0200
+@@ -4,7 +4,7 @@
+ */
+
+ #include "protml.h"
+-
++#include "prot_tml.h"
+
+ void
+ getsize(ifp, maxspc, numsite, commentp)
+@@ -18,7 +18,7 @@
+
+ if (fgets(line, BUFLINE, ifp) != NULL) {
+ if (sscanf(line, "%d %d", maxspc, numsite) == 2) {
+- for (cp = line; isdigit(*cp) || isspace(*cp) && *cp != '\0'; cp++)
++ for (cp = line; isdigit(*cp) || isspace(*cp) /*&& *cp != '\0'*/; cp++)
+ ;
+ *commentp = new_cvector(strlen(cp) + 1);
+ if (*cp != '\0') {
+diff -ubrN src.orig/Makefile src/Makefile
+--- src.orig/Makefile 1996-07-02 16:56:36.000000000 +0200
++++ src/Makefile 2006-09-10 15:20:27.000000000 +0200
+@@ -1,10 +1,13 @@
+-INSTALLDIR = ./.. # /usr/local/bin/molphy
++.SUFFIXES: .o .c
++
++INSTALLDIR = /usr/local/bin/molphy
+
+ CC = gcc # cc, gcc, c89
+-CFLAGS = -O # -O4 or +O
++CFLAGS = -O3 # -O4 or +O
+ DEFINE = #
+-LIBS = -lm # -lM
+-CP = cp # copy command
++LIBS = -lm -lc
++# CP = cp -a
++CP = ln -s
+ NUCLE = -DNUC
+ NJLE = -DNJ
+ SDLE = -DSD
+@@ -82,102 +85,102 @@
+
+ # protml nucml
+
+-protml.o : protml.c protml.h molphy.h
++protml.o : protml.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c protml.c
+ Nucml.c : protml.c optimtpm.c abratio.c
+ $(CP) protml.c Nucml.c
+-Nucml.o : Nucml.c protml.h molphy.h optimtpm.c abratio.c
++Nucml.o : Nucml.c protml.h molphy.h optimtpm.c abratio.c matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nucml.c
+-getseq.o : getseq.c protml.h molphy.h
++getseq.o : getseq.c protml.h molphy.h prot_tml.h
+ $(CC) $(CFLAGS) $(DEFINE) -c getseq.c
+-seqproc.o : seqproc.c protml.h molphy.h
++seqproc.o : seqproc.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c seqproc.c
+-tranprb.o : tranprb.c protml.h molphy.h
++tranprb.o : tranprb.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c tranprb.c
+ Ntranprb.c : tranprb.c
+ $(CP) tranprb.c Ntranprb.c
+-Ntranprb.o : Ntranprb.c protml.h molphy.h
++Ntranprb.o : Ntranprb.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Ntranprb.c
+-distan.o : distan.c protml.h molphy.h
++distan.o : distan.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c distan.c
+ Ndistan.c : distan.c
+ $(CP) distan.c Ndistan.c
+-Ndistan.o : Ndistan.c protml.h molphy.h
++Ndistan.o : Ndistan.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Ndistan.c
+-mltree.o : mltree.c protml.h molphy.h
++mltree.o : mltree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mltree.c
+-altree.o : altree.c protml.h molphy.h
++altree.o : altree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c altree.c
+-qltree.o : qltree.c protml.h molphy.h
++qltree.o : qltree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c qltree.c
+-sltree.o : sltree.c protml.h molphy.h
++sltree.o : sltree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c sltree.c
+-njtree.o : njtree.c protml.h molphy.h
++njtree.o : njtree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c njtree.c
+-njmtree.o : njmtree.c protml.h molphy.h
++njmtree.o : njmtree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c njmtree.c
+-mlklhd.o : mlklhd.c protml.h molphy.h
++mlklhd.o : mlklhd.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mlklhd.c
+ Nmlklhd.c : mlklhd.c
+ $(CP) mlklhd.c Nmlklhd.c
+-Nmlklhd.o : Nmlklhd.c protml.h molphy.h
++Nmlklhd.o : Nmlklhd.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nmlklhd.c
+-prtree.o : prtree.c protml.h molphy.h
++prtree.o : prtree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c prtree.c
+-pstree.o : pstree.c protml.h molphy.h
++pstree.o : pstree.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c pstree.c
+
+-protproc.o : protproc.c protml.h molphy.h
++protproc.o : protproc.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c protproc.c
+-nucproc.o : nucproc.c protml.h molphy.h
++nucproc.o : nucproc.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c nucproc.c
+-dyhfjtt.o : dyhfjtt.c protml.h molphy.h
++dyhfjtt.o : dyhfjtt.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c dyhfjtt.c
+-mtrev24.o : mtrev24.c protml.h molphy.h
++mtrev24.o : mtrev24.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mtrev24.c
+
+ # protst nucst
+
+-protst.o : protst.c protst.h molphy.h
++protst.o : protst.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c protst.c
+ Nucst.c : protst.c
+ $(CP) protst.c Nucst.c
+-Nucst.o : Nucst.c protst.h molphy.h
++Nucst.o : Nucst.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nucst.c
+
+-seqstat.o : seqstat.c protst.h molphy.h
++seqstat.o : seqstat.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c seqstat.c
+ Nseqstat.c : seqstat.c
+ $(CP) seqstat.c Nseqstat.c
+-Nseqstat.o : Nseqstat.c protst.h molphy.h
++Nseqstat.o : Nseqstat.c protst.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nseqstat.c
+
+ # tridist njdist
+
+-tridist.o : tridist.c tridist.h molphy.h
++tridist.o : tridist.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c tridist.c
+-triproc.o : triproc.c tridist.h molphy.h
++triproc.o : triproc.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c triproc.c
+ Njdist.c : tridist.c
+ $(CP) tridist.c Njdist.c
+-Njdist.o : Njdist.c tridist.h molphy.h
++Njdist.o : Njdist.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) $(NJLE) -c Njdist.c
+-njproc.o : njproc.c tridist.h molphy.h
++njproc.o : njproc.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c njproc.c
+ sddist.o : sddist.c sddist.h molphy.h
+ $(CC) $(CFLAGS) $(DEFINE) $(SDLE) -c sddist.c
+ sdproc.o : sdproc.c sddist.h molphy.h
+ $(CC) $(CFLAGS) $(DEFINE) -c sdproc.c
+-distproc.o : distproc.c tridist.h molphy.h
++distproc.o : distproc.c tridist.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c distproc.c
+ Dpstree.c : pstree.c
+ $(CP) pstree.c Dpstree.c
+-Dpstree.o : Dpstree.c tridist.h molphy.h
++Dpstree.o : Dpstree.c tridist.h molphy.h protml.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) $(NJLE) -c Dpstree.c
+
+ # totalml
+
+-totalml.o : totalml.c totalml.h molphy.h
++totalml.o : totalml.c totalml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c totalml.c
+
+ # tmlprot
+@@ -192,11 +195,11 @@
+
+ Prottpm.c : protml.c
+ $(CP) protml.c Prottpm.c
+-Prottpm.o : Prottpm.c protml.h molphy.h
++Prottpm.o : Prottpm.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) -DTPM $(DEFINE) -c Prottpm.c
+ Nuctpm.c : protml.c
+ $(CP) protml.c Nuctpm.c
+-Nuctpm.o : Nuctpm.c protml.h molphy.h
++Nuctpm.o : Nuctpm.c protml.h molphy.h matrixut.h
+ $(CC) $(CFLAGS) -DTPM $(NUCLE) $(DEFINE) -c Nuctpm.c
+
+ tpmproc.o : tpmproc.c protml.h molphy.h
+@@ -234,11 +237,12 @@
+
+ matrixut.o : matrixut.c matrixut.h
+ $(CC) $(CFLAGS) $(DEFINE) -c matrixut.c
+-mygetopt.o : mygetopt.c
++mygetopt.o : mygetopt.c molphy.h
+ $(CC) $(CFLAGS) $(DEFINE) -c mygetopt.c
+
+ install : $(PRGS)
+- $(CP) $(PRGS) $(INSTALLDIR)
++ mkdir -p $(INSTALLDIR)
++ cp -a $(PRGS) $(INSTALLDIR)
+ cd $(INSTALLDIR); \
+ chmod 755 $(PRGS)
+
+@@ -272,6 +276,15 @@
+ rcp [a-z]*.c *.h Makefile sunmh:/home/sunmh/adachi/work/molphybeta
+
+ RMSRC :
+- rm bdate.c compcrit.c dmlproc.c protdml.c protdml.h ptnlkl.c \
+- sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c tpmproc.c \
++# rm bdate.c compcrit.c protdml.h ptnlkl.c \
++# sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c \
++# triadml.c
++ @echo This target intends to remove the following files
++ @echo bdate.c compcrit.c protdml.h ptnlkl.c \
++ sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c \
+ triadml.c
++ @echo This is prevented because I consider it to be a bad idea to remove sources.
++
++## The following file is unused in original molphy and there are just plain
++## dependencies in the arb pachage because it was automatically generated
++## mtrev22.o: protml.h molphy.h matrixut.h
+diff -ubrN src.orig/molphy.h src/molphy.h
+--- src.orig/molphy.h 1996-07-02 16:56:01.000000000 +0200
++++ src/molphy.h 2006-09-10 15:20:27.000000000 +0200
+@@ -17,7 +17,7 @@
+ #define DIR_CHAR '/' /* directory separator '/' (UNIX) */
+ #else
+ #define SW_CHAR '/' /* switch charcter '/' (MSDOS) */
+-#define DIR_CHAR '\' /* directory separator '\' (MSDOS) */
++#define DIR_CHAR '\\' /* directory separator '\' (MSDOS) */
+ #endif
+
+ #ifdef RAND_MAX
+diff -ubrN src.orig/Nucml.c src/Nucml.c
+--- src.orig/Nucml.c 1996-07-02 16:56:00.000000000 +0200
++++ src/Nucml.c 2006-09-10 15:20:27.000000000 +0200
+@@ -540,7 +540,7 @@
+ }
+
+
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
+@@ -1124,6 +1124,7 @@
+ prtopology(Ctree);
+ resulttree(Ctree);
+ pstree(Epsfp, Ctree);
++ fputcphylogeny(Trefp, Ctree);
+ FREE_LPMATRIX(Lklptrn);
+
+ } else if (Njoin_optn) { /* NJ MODE */
+diff -ubrN src.orig/nucproc.c src/nucproc.c
+--- src.orig/nucproc.c 1996-07-02 16:56:00.000000000 +0200
++++ src/nucproc.c 2006-09-10 15:20:27.000000000 +0200
+@@ -20,9 +20,7 @@
+ };
+
+
+-int
+-isacid(c)
+-char c;
++int isacid(char c)
+ {
+ /* nuc */
+ switch (c) {
+diff -ubrN src.orig/Nucst.c src/Nucst.c
+--- src.orig/Nucst.c 1996-07-02 16:56:00.000000000 +0200
++++ src/Nucst.c 2006-09-10 15:20:27.000000000 +0200
+@@ -136,31 +136,31 @@
+ }
+
+
+-#if 0
+-void
+-header(ofp, maxspc, numsite, commentp)
+-FILE *ofp;
+-int *maxspc;
+-int *numsite;
+-char **commentp;
+-{
+- time_t ct;
+- char *datetime, *ip, *jp;
+-
+- fprintf(ofp, "%s %s ", Prog_name, VERSION);
+-
+- ct = time(NULL);
+- datetime = ctime(&ct);
+- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++;
+- *ip = '\0';
+- fputs(datetime + 4, ofp);
+- fputs(" ", ofp);
+- fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp);
+- free_cvector(*commentp);
+-} /*_ header */
+-#endif
++/* #if 0 */
++/* void */
++/* header(ofp, maxspc, numsite, commentp) */
++/* FILE *ofp; */
++/* int *maxspc; */
++/* int *numsite; */
++/* char **commentp; */
++/* { */
++/* time_t ct; */
++/* char *datetime, *ip, *jp; */
++
++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */
++
++/* ct = time(NULL); */
++/* datetime = ctime(&ct); */
++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */
++/* *ip = '\0'; */
++/* fputs(datetime + 4, ofp); */
++/* fputs(" ", ofp); */
++/* fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp); */
++/* free_cvector(*commentp); */
++/* } / *_ header * / */
++/* #endif */
+
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
+diff -ubrN src.orig/Nuctpm.c src/Nuctpm.c
+--- src.orig/Nuctpm.c 1996-07-02 16:56:00.000000000 +0200
++++ src/Nuctpm.c 2006-09-10 15:20:27.000000000 +0200
+@@ -540,7 +540,7 @@
+ }
+
+
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
+@@ -1124,6 +1124,7 @@
+ prtopology(Ctree);
+ resulttree(Ctree);
+ pstree(Epsfp, Ctree);
++ fputcphylogeny(Trefp, Ctree);
+ FREE_LPMATRIX(Lklptrn);
+
+ } else if (Njoin_optn) { /* NJ MODE */
+diff -ubrN src.orig/protml.c src/protml.c
+--- src.orig/protml.c 1996-07-02 16:56:00.000000000 +0200
++++ src/protml.c 2006-09-10 15:20:27.000000000 +0200
+@@ -540,7 +540,7 @@
+ }
+
+
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
+@@ -1124,6 +1124,7 @@
+ prtopology(Ctree);
+ resulttree(Ctree);
+ pstree(Epsfp, Ctree);
++ fputcphylogeny(Trefp, Ctree);
+ FREE_LPMATRIX(Lklptrn);
+
+ } else if (Njoin_optn) { /* NJ MODE */
+diff -ubrN src.orig/protst.c src/protst.c
+--- src.orig/protst.c 1996-07-02 16:56:00.000000000 +0200
++++ src/protst.c 2006-09-10 15:20:27.000000000 +0200
+@@ -136,31 +136,31 @@
+ }
+
+
+-#if 0
+-void
+-header(ofp, maxspc, numsite, commentp)
+-FILE *ofp;
+-int *maxspc;
+-int *numsite;
+-char **commentp;
+-{
+- time_t ct;
+- char *datetime, *ip, *jp;
+-
+- fprintf(ofp, "%s %s ", Prog_name, VERSION);
+-
+- ct = time(NULL);
+- datetime = ctime(&ct);
+- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++;
+- *ip = '\0';
+- fputs(datetime + 4, ofp);
+- fputs(" ", ofp);
+- fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp);
+- free_cvector(*commentp);
+-} /*_ header */
+-#endif
++/* #if 0 */
++/* void */
++/* header(ofp, maxspc, numsite, commentp) */
++/* FILE *ofp; */
++/* int *maxspc; */
++/* int *numsite; */
++/* char **commentp; */
++/* { */
++/* time_t ct; */
++/* char *datetime, *ip, *jp; */
++
++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */
++
++/* ct = time(NULL); */
++/* datetime = ctime(&ct); */
++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */
++/* *ip = '\0'; */
++/* fputs(datetime + 4, ofp); */
++/* fputs(" ", ofp); */
++/* fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp); */
++/* free_cvector(*commentp); */
++/* } / *_ header * / */
++/* #endif */
+
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
+diff -ubrN src.orig/prot_tml.h src/prot_tml.h
+--- src.orig/prot_tml.h 1970-01-01 01:00:00.000000000 +0100
++++ src/prot_tml.h 2006-09-10 15:20:27.000000000 +0200
+@@ -0,0 +1,241 @@
++#ifndef P_
++# if defined(__STDC__) || defined(__cplusplus)
++# define P_(s) s
++# else
++# define P_(s) ()
++# endif
++#else
++# error P_ already defined elsewhere
++#endif
++
++
++/* getseq.c */
++void getsize P_((FILE *ifp, int *maxspc, int *numsite, char **commentp));
++void getid P_((FILE *ifp, char **identif, char **sciname, char **engname, int *nl, int *notu));
++void getsites P_((FILE *ifp, cmatrix seqchar, int numsite, int *nl, int *notu));
++void getseq P_((FILE *ifp, char **identif, char **sciname, char **engname, cmatrix seqchar, int maxspc, int numsite));
++void getidsites P_((FILE *ifp, cmatrix identif, cmatrix seqchar, int numsite, int *nl, int *notu));
++void getseqs P_((FILE *ifp, char **identif, cmatrix seqchar, int maxspc, int numsite));
++void getseqi P_((FILE *ifp, char **identif, cmatrix seqchar, int maxspc, int numsite));
++void fputid P_((FILE *ofp, char *name, int maxcolumn));
++void prsequence P_((FILE *ofp, char **identif, char **seqchar, int maxspc, int maxsite));
++
++/* seqproc.c */
++void convseq P_((imatrix seqconint, int maxspc, int numptrn));
++void getfreqepm P_((cmatrix seqchar, double *freqemp, int maxspc, int maxsite));
++void convfreq P_((double *freqemp));
++void radixsort P_((cmatrix seqchar, ivector alias, int maxspc, int maxsite, int *numptrn));
++void condenceseq P_((cmatrix seqchar, ivector alias, imatrix seqconint, ivector weight, int maxspc, int maxsite, int numptrn));
++void getnumsites P_((imatrix seqconint, ivector numsites, ivector weight, int numspc, int numptrn));
++void prcondenceseq P_((char **identif, imatrix seqconint, ivector weight, int numspc, int numsite, int numptrn));
++
++/* mltree.c */
++Node **new_npvector P_((int n));
++void free_npvector P_((Node **v));
++Tree *new_tree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++int getbuftree P_((int numspc, cmatrix identif));
++void changedistan P_((dmatrix distanmat, dvector distanvec, int numspc));
++void getproportion P_((double *proportion, dvector distanvec, int maxpair));
++Infotree *newinfotrees P_((int numtree, int buftree));
++Infoaltree *newinfoaltrees P_((int numaltree, int buftree));
++void getnumtree P_((FILE *ifp, int *numtree));
++void getusertree P_((FILE *ifp, cvector strtree, int buftree));
++Node *internalnode P_((Tree *tr, char **cpp, int *ninode, char *st));
++void constructtree P_((Tree *tr, cvector strtree));
++void prcurtree P_((Tree *tr));
++void pathing P_((Tree *tr));
++void lslength P_((Tree *tr, dvector distanvec, int numspc));
++void slslength P_((Tree *tr, dmatrix dmat, int ns));
++void fmlength P_((Tree *tr, dmatrix dmat, int ns));
++void resulttree P_((Tree *tr));
++void bootstrap P_((Infotree *infotrs, LPMATRIX lklptrn));
++void tabletree P_((Infotree *infotrs, LPMATRIX lklptrn));
++void tableinfo P_((Infotree *infotrs));
++void rerootq P_((Tree *tr, int numspc));
++void outlklhd P_((LPMATRIX lklptrn));
++void putsortseq P_((Tree *tr));
++
++/* altree.c */
++Tree *new_atree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++Node *new_dnode P_((void));
++Node *new_anode P_((void));
++Node ***new_nodematrix P_((int nrow, int ncol));
++void free_nodematrix P_((Node ***m));
++void aproxlkl P_((Tree *tr));
++void aproxlkl P_((Tree *tr));
++void praproxlkl P_((Tree *tr));
++void aproxtree P_((Tree *tr, int ntr));
++void wedge P_((Tree *tr, int onode, Node **poolnode, Node **addposition, ivector poolorder, Node *op));
++void autoconstruction P_((Tree *tr, int onode, Node **poolnode, Node **addposition, ivector poolorder));
++Node *inbranode P_((Tree *tr, char **cpp, int *nenode, int numorder, Node ***poolnode2, cvector st));
++void streeinit P_((Tree *tr, cvector strtree, Node **poolnode, Node **addposition, ivector poolorder));
++void atreeinit P_((Tree *tr, Node **poolnode, Node **addposition, ivector poolorder));
++void tablealtree P_((int nt));
++
++/* qltree.c */
++Infoqltree *newinfoqltrees P_((int n, int maxbrnch));
++Infoaddtree *newinfoaddtree P_((int buftree));
++void initturn P_((Tree *tr));
++void randturn P_((Tree *tr));
++void convertdistan P_((Tree *tr, int numspc, dmatrix distanmat, dvector distanvec));
++void praproxlkl2 P_((FILE *fp, Tree *tr));
++int addotu P_((Tree *tr, Node *cp, Node *np, Node *ip, int cnspc));
++int addotual P_((Tree *tr, Node *cp, Node *np, Node *ip, dvector lengs));
++void roundtree P_((Tree *tr, int cnspc, Infoqltree *infoqltrees, Infoqltree *qhead, Infoqltree *qtail));
++void qtreeinit P_((Tree *tr));
++void tableaddtree P_((Infoaddtree *head, int numaddtree));
++
++/* sltree.c */
++Tree *new_stree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++Infosltree *newinfosltrees P_((int num, int maxbrnch));
++void insertbranch P_((Node *ibp, Node *np));
++void deletebranch P_((Node *ibp, Node *np));
++void movebranch P_((Node *jbp, Node *ip));
++void removebranch P_((Node *jbp, Node *ip));
++void subpathing P_((Node *np));
++void copylength P_((Tree *tr, dvector lengs));
++Node *sdml P_((Tree *tr, Node *op));
++void decomposition P_((Tree *tr, int n, Infosltree *infosltrees));
++void stardecomp P_((Tree *tr, int maxibrnch));
++dcube new_dcubesym P_((int nrow, int ncol));
++void free_dcubesym P_((dcube c));
++void ystardecomp P_((Tree *tr));
++void xstardecomp P_((Tree *tr));
++
++/* njtree.c */
++Tree *new_njtree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint));
++void free_njtree P_((Tree *tr, int maxspc, int maxibrnch));
++double emledis P_((double dis, Node *ip, Node *kp));
++double imledis P_((double dis, Node *ip, Node *kp));
++void redmat P_((dmatrix dmat, double dij, Node **psotu, ivector otu, int restsp, int ii, int jj, int ns));
++void enjtree P_((Tree *tr, dmatrix distan, int ns, boolean flag));
++
++/* njmtree.c */
++void initsubplkl P_((Node *op));
++void mlepartlen P_((Node *ip, Node *jp, Node **rotup, int nr, int ns));
++void remldmat P_((dmatrix dmat, double dij, Node **psotu, Node **rotup, int otui, int otuj, int ns));
++void njmtree P_((Tree *tr, dmatrix distan, int ns, boolean flag));
++
++/* prtree.c */
++void putctopology P_((Tree *tr));
++void fputctopology P_((FILE *fp, Tree *tr));
++void fputcphylogeny P_((FILE *fp, Tree *tr));
++void prtopology P_((Tree *tr));
++void strctree P_((Tree *tr, char *ltree));
++
++/* pstree.c */
++void psdicter P_((FILE *fp));
++void pstree P_((FILE *fp, Tree *tr));
++
++/* matrixut.c */
++void maerror P_((char *message));
++fvector new_fvector P_((int n));
++fmatrix new_fmatrix P_((int nrow, int ncol));
++fcube new_fcube P_((int ntri, int nrow, int ncol));
++void free_fvector P_((fvector v));
++void free_fmatrix P_((fmatrix m));
++void free_fcube P_((fcube c));
++dvector new_dvector P_((int n));
++dmatrix new_dmatrix P_((int nrow, int ncol));
++dcube new_dcube P_((int ntri, int nrow, int ncol));
++void free_dvector P_((dvector v));
++void free_dmatrix P_((dmatrix m));
++void free_dcube P_((dcube c));
++cvector new_cvector P_((int n));
++cmatrix new_cmatrix P_((int nrow, int ncol));
++ccube new_ccube P_((int ntri, int nrow, int ncol));
++void free_cvector P_((cvector v));
++void free_cmatrix P_((cmatrix m));
++void free_ccube P_((ccube c));
++ivector new_ivector P_((int n));
++imatrix new_imatrix P_((int nrow, int ncol));
++icube new_icube P_((int ntri, int nrow, int ncol));
++void free_ivector P_((ivector v));
++void free_imatrix P_((imatrix m));
++void free_icube P_((icube c));
++
++/* mygetopt.c */
++int mygetopt P_((int argc, char **argv, char *optstring));
++
++/* protml.c */
++void copyright P_((void));
++void usage P_((void));
++void helpinfo P_((void));
++int main P_((int argc, char **argv));
++void header P_((FILE *ofp, int *maxspc, int *numsite, char **commentp));
++void headerd P_((FILE *ofp, int *maxspc, int *numsite, char **commentp));
++void pml P_((FILE *ifp, FILE *ofp));
++
++/* protproc.c */
++int isacid P_((int c));
++int acid2int P_((int c));
++char acid2chint P_((int c));
++char chint2acid P_((int c));
++char int2acid P_((int i));
++
++/* dyhfjtt.c */
++void dyhfjtt P_((dmattpmty r, double *f, boolean flag));
++
++/* mtrev24.c */
++void mtrev P_((dmattpmty r, double *f));
++
++/* tranprb.c */
++void elmhes P_((dmattpmty a, int *ordr, int n));
++void eltran P_((dmattpmty a, dmattpmty zz, int *ordr, int n));
++void hqr2 P_((int n, int low, int hgh, int *err, dmattpmty h, dmattpmty zz, double *wr, double *wi));
++void readrsrf P_((dmattpmty r, dvectpmty f, int n));
++void tpmonepam P_((dmattpmty a, double *f));
++void luinverse P_((dmattpmty omtrx, dmattpmty imtrx, int size));
++void mproduct P_((dmattpmty am, dmattpmty bm, dmattpmty cm, int na, int nb, int nc));
++void preigen P_((void));
++void checkevector P_((dmattpmty imtrx, int nn));
++void getrsr P_((dmattpmty a, dvectpmty ftpm));
++void tranprobmat P_((void));
++void varitpm P_((void));
++void prfreq P_((void));
++void tprobmtrx P_((double arc, dmattpmty tpr));
++void tprobmtrxt P_((double arc, dmattpmty tpr));
++void tdiffmtrx P_((double arc, dmattpmty tpr, dmattpmty td1, dmattpmty td2));
++void tprobmtrx2 P_((double arc, dmattpmty tpr));
++void tdiffmtrx2 P_((double arc, dmattpmty tpr, dmattpmty td1, dmattpmty td2));
++
++/* distan.c */
++void distance P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite));
++void lddistance P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite));
++void tdistan P_((ivector seqi, ivector seqj, dmatrix probk, ivector weight, int nptrn, double *len, double *lvari, dcube triprob));
++void tdistan2 P_((ivector seqi, ivector seqj, ivector seqk, ivector seqw, int nsite, double *len, double *lvari, dcube triprob));
++void tridistance P_((dmatrix distanmat, imatrix seqconint, ivector weight, int maxspc, int numptrn));
++void tridistance2 P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite));
++void putdistance P_((cmatrix identif, cmatrix sciname, cmatrix engname, dmatrix distanmat, int maxspc));
++void checkseq P_((imatrix seqconint, int maxspc, int numptrn));
++
++/* mlklhd.c */
++double probnormal P_((double z));
++double uprobnormal P_((double z));
++void copypart1 P_((Node *op, Node *cp));
++void prodpart1 P_((Node *op, Node *cp));
++void prodpart P_((Node *op));
++void partilkl P_((Node *op));
++void partelkl P_((Node *op));
++void partelkl2 P_((Node *op));
++void initpartlkl P_((Tree *tr));
++void regupartlkl P_((Tree *tr));
++void mlibranch P_((Node *op, double eps, int nloop));
++void mlebranch P_((Node *op, double eps, int nloop));
++void mlebranch2 P_((Node *op, double eps, int nloop));
++void evallkl P_((Node *op));
++Node *mlikelihood P_((Tree *tr));
++void ribranch P_((Node *op));
++Node *relibranch P_((Node *op));
++void mlvalue P_((Tree *tr, Infotree *infotrs));
++void reroot P_((Tree *tr, Node *rp));
++void sorttree P_((Tree *tr, Node *rp));
++void chroot P_((Tree *tr, int s1, int s2));
++void noexch P_((Node *rp, ivector exchstate));
++void reliml P_((Tree *tr, Node *op, double lklorg, LPVECTOR mlklptrn, double *rel));
++void localbp P_((dmatrix reliprob, LPVECTOR mlklptrn, LPCUBE rlklptrn, ivector whichml, int nb, int ns));
++void reliabranch P_((Tree *tr));
++void annealing P_((Tree *tr));
++void qlrsearch P_((Tree *tr));
++
++#undef P_
+diff -ubrN src.orig/pstree.c src/pstree.c
+--- src.orig/pstree.c 1996-07-02 16:56:00.000000000 +0200
++++ src/pstree.c 2006-09-10 15:20:27.000000000 +0200
+@@ -153,10 +153,10 @@
+ if (len == 0) len = 1;
+ if (cp->descen) x += len;
+ if (cp->isop == NULL) { /* external node */
+- (Sciname[cp->num][0] != '\0') ?
++ (Sciname[cp->num] && Sciname[cp->num][0] != '\0') ? /* @@@OLIVER */
+ (name = Sciname[cp->num]) : (name = Identif[cp->num]);
+ s = (int)(fontw * (strlen(name) + 1) + 10);
+- if (Engname[cp->num][0] != '\0') {
++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */
+ s += (int)(fontw * (strlen(Engname[cp->num]) + 1));
+ }
+ xs = x + s;
+@@ -232,12 +232,12 @@
+ fprintf(fp, "n %3d %3d m %3d %3d l s ", x - len, y, x, y);
+ fprintf(fp, " %3d %3d m", x + (int)fontw, y-fontc);
+ fprintf(fp, " %% %3d\n", cp->num+1);
+- if (Sciname[cp->num][0] == '\0') {
++ if (Sciname[cp->num]== 0 || Sciname[cp->num][0] == '\0') { /* @@@OLIVER */
+ fprintf(fp, " Fid ff %d sf (%s) sh", fonts, Identif[cp->num]);
+ } else {
+ fprintf(fp, " Fsc ff %d sf (%s) sh", fonts, Sciname[cp->num]);
+ }
+- if (Engname[cp->num][0] != '\0') {
++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */
+ fprintf(fp, " Fid ff %d sf ( %s) sh\n",fonts,Engname[cp->num]);
+ } else {
+ fprintf(fp, "\n");
+diff -ubrN src.orig/qltree.c src/qltree.c
+--- src.orig/qltree.c 1996-07-02 16:56:00.000000000 +0200
++++ src/qltree.c 2006-09-10 15:20:27.000000000 +0200
+@@ -140,7 +140,7 @@
+ } /*_ praproxlkl2 */
+
+
+-addotu(tr, cp, np, ip, cnspc)
++int addotu(tr, cp, np, ip, cnspc)
+ Tree *tr;
+ Node *cp, *np, *ip;
+ int cnspc;
+diff -ubrN src.orig/totalml.c src/totalml.c
+--- src.orig/totalml.c 1996-07-02 16:56:00.000000000 +0200
++++ src/totalml.c 2006-09-10 15:20:27.000000000 +0200
+@@ -40,31 +40,31 @@
+ }
+
+
+-#if 0
+-void
+-header(ofp, numseqs, allsite, commentp)
+-FILE *ofp;
+-int *numseqs;
+-int *allsite;
+-char **commentp;
+-{
+- time_t ct;
+- char *datetime, *ip, *jp;
++/* #if 0 */
++/* void */
++/* header(ofp, numseqs, allsite, commentp) */
++/* FILE *ofp; */
++/* int *numseqs; */
++/* int *allsite; */
++/* char **commentp; */
++/* { */
++/* time_t ct; */
++/* char *datetime, *ip, *jp; */
++
++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */
++
++/* ct = time(NULL); */
++/* datetime = ctime(&ct); */
++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */
++/* *ip = '\0'; */
++/* fputs(datetime + 4, ofp); */
++/* fprintf(ofp, " %d data %d sites.\n", *numseqs, *allsite); */
++/* / * fprintf(ofp, " %d data %d sites. %s\n", *numseqs, *allsite, *commentp); * / */
++/* } / *_ header * / */
++/* #endif */
+
+- fprintf(ofp, "%s %s ", Prog_name, VERSION);
+
+- ct = time(NULL);
+- datetime = ctime(&ct);
+- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++;
+- *ip = '\0';
+- fputs(datetime + 4, ofp);
+- fprintf(ofp, " %d data %d sites.\n", *numseqs, *allsite);
+-/* fprintf(ofp, " %d data %d sites. %s\n", *numseqs, *allsite, *commentp); */
+-} /*_ header */
+-#endif
+-
+-
+-void
++ void
+ header(ofp, maxspc, numsite, commentp)
+ FILE *ofp;
+ int *maxspc;
Added: trunk/packages/molphy/trunk/debian/patches/utl_Install.diff
===================================================================
--- trunk/packages/molphy/trunk/debian/patches/utl_Install.diff (rev 0)
+++ trunk/packages/molphy/trunk/debian/patches/utl_Install.diff 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,8 @@
+--- utl/Install.orig 1996-07-02 16:56:02.000000000 +0200
++++ utl/Install 2006-09-10 15:20:27.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ # Usage: Install install_directory
+
Added: trunk/packages/molphy/trunk/debian/protml.1
===================================================================
--- trunk/packages/molphy/trunk/debian/protml.1 (rev 0)
+++ trunk/packages/molphy/trunk/debian/protml.1 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,79 @@
+'\" t
+.\" ** The above line should force tbl to be a preprocessor **
+.\" Copyright (C), 2001, Andreas Tille <tille at debian.org>
+.\"
+.\" You may distribute under the terms of the GNU General Public
+.\" License as specified in the file COPYING that comes with the
+.\" man_db distribution.
+.\"
+.\"
+.TH MolPhy 1 "November 7, 2001" "MOLecular PHYlogenetics"
+.SH NAME
+.B MolPhy
+\- program package for MOLecular PHYlogenetics
+
+Molphy consists of several programs:
+
+.B protml
+\- Maximum Likelihood Inference of Protein Phylogeny
+.br
+.B nucml
+\- Maximum Likelihood Inference of Nucleic Acid Phylogeny
+.br
+.B protst
+\- Basic Statistics of Protein Sequences
+.br
+.B nucst
+\- Basic Statistics of Nucleic Acid Sequence
+.br
+.B njdist
+\- Neighbor Joining Phylogeny from Distance Matrix
+.br
+.B totalml
+\- Total ML Inference of Molecular Phylogeny
+
+.SH SYNOPSIS
+.B protml
+.RB [switches]
+.IR sequence_file
+.IR [topology_file]
+.br
+.B nucml
+.RB [switches]
+.IR sequence_file
+.IR [topology_file]
+.br
+.B protst
+.RB [switches]
+.IR sequence_file
+.br
+.B nucst
+.RB [switches]
+.IR sequence_file
+.br
+.B njdist
+.RB [switches]
+.IR distance_matrix_file
+.br
+.B totalml
+.RB [switches]
+.IR LLS_files
+
+.SH DESCRIPTION
+This is the Debian GNU/Linux version of the
+MOLPHY (ProtML) distribution, version 2.3.
+Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa.
+All rights reserved.
+
+MOLPHY is a program package for MOLecular PHYlogenetics.
+
+ProtML is a main program in MOLPHY for inferring evolutionary trees from
+PROTein (amino acid) sequences by using the Maximum Likelihood method.
+
+Each single program has a
+.B -h
+switch which shows some help.
+
+.SH AUTHOR
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/molphy/trunk/debian/rules
===================================================================
--- trunk/packages/molphy/trunk/debian/rules (rev 0)
+++ trunk/packages/molphy/trunk/debian/rules 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+# debian/rules for molphy using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+pkg=molphy
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+clean::
+ cd src; make clean
+
+# Use makefile in subdir
+# Remark: mentioning INSTALLDIR does not have any effect because the
+# install target is not called by cdbs by default; just lets use debian/install
+# DEB_MAKE_INVOKE = cd src; $(DEB_MAKE_ENVVARS) make INSTALLDIR=../debian/$(pkg)/usr/bin $(if $(DEB_MAKE_MAKEFILE), -f $(DEB_MAKE_MAKEFILE),) -C $(DEB_BUILDDIR) CFLAGS=$(if $(CFLAGS_$(cdbs_curpkg)),"$(CFLAGS_$(cdbs_curpkg))","$(CFLAGS)") CXXFLAGS=$(if $(CXXFLAGS_$(cdbs_curpkg)),"$(CXXFLAGS_$(cdbs_curpkg))","$(CXXFLAGS)")
+DEB_MAKE_INVOKE = cd src; $(DEB_MAKE_ENVVARS) make $(if $(DEB_MAKE_MAKEFILE), -f $(DEB_MAKE_MAKEFILE),) -C $(DEB_BUILDDIR) CFLAGS=$(if $(CFLAGS_$(cdbs_curpkg)),"$(CFLAGS_$(cdbs_curpkg))","$(CFLAGS)") CXXFLAGS=$(if $(CXXFLAGS_$(cdbs_curpkg)),"$(CXXFLAGS_$(cdbs_curpkg))","$(CXXFLAGS)")
+
+install/molphy::
+ ### replace perl path from /usr/local/bin to /usr/bin which is
+ ### in principle what utl/Install is doing
+ # for utl in `ls utl/*.pl` ; do \
+ # sed 's?#!/usr/local/bin/perl?#!/usr/bin/perl?' $${utl} > `pwd`/debian/`dh_listpackages`/usr/bin/`basename $${utl} .pl` ; \
+ # done
+ ### But why not using the original script ??
+ cd utl; ./Install ../debian/$(pkg)/usr/bin
Property changes on: trunk/packages/molphy/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/molphy/trunk/debian/tests/compare/README.compare
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/README.compare (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/README.compare 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,13 @@
+I've got those test examples from
+ http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/testdata
+The original files in the compare directory where build with molphy 2.2.
+I found out that the results with version 2.3b3 differ slightly in
+the precision of some floats. I think this is OK.
+
+On the other hand there were some different trees created in
+ test4.nj, test6.mls, test7.mls and test15.nj
+So I leave here the original example file named <filename>-2.2 and just
+leave it to some more educated people in phylogenetic trees to decide what´s
+correct here. In my opinion this are just different representations
+of one tree but please report it to <tille at debian.org> if you doubt that.
+
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.dis
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.dis (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.dis 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,61 @@
+15 409 sites JTT test15.ptn
+Homo
+ 0.000000000000 0.036941950975 0.151849499085 0.175452276938 0.186308284045
+ 0.178557231654 0.175460021426 0.171381705808 0.242558390091 0.239818426034
+ 0.711229145466 0.627975207365 0.657474744501 0.681818041556 0.738465099336
+Xenopus
+ 0.036941950975 0.000000000000 0.164701173415 0.190703594342 0.197551671507
+ 0.184308599151 0.182349699549 0.164080100858 0.255776516678 0.244680817390
+ 0.715551867177 0.644715916524 0.649699323398 0.692484941077 0.756225268778
+Drosophil
+ 0.151849499085 0.164701173415 0.000000000000 0.125772039669 0.215277763145
+ 0.211175855041 0.227217806440 0.204178994811 0.256220603581 0.255322597474
+ 0.719922660503 0.628402341913 0.635238587361 0.650765472456 0.728333862467
+Artemia
+ 0.175452276938 0.190703594342 0.125772039669 0.000000000000 0.216896015811
+ 0.222175650450 0.247563133706 0.219781287346 0.273666339087 0.290368846607
+ 0.764658513106 0.661840294620 0.694883040771 0.665517479246 0.744690215581
+Saccharom
+ 0.186308284045 0.197551671507 0.215277763145 0.216896015811 0.000000000000
+ 0.091449159965 0.160750248794 0.145644518755 0.280385638946 0.278657537403
+ 0.733098885492 0.643129634435 0.664012590502 0.693115324686 0.754796557471
+Candida
+ 0.178557231654 0.184308599151 0.211175855041 0.222175650450 0.091449159965
+ 0.000000000000 0.138031643786 0.122675348331 0.273008128171 0.278020382072
+ 0.713140264266 0.625663809960 0.657954595852 0.683280435752 0.745473130516
+Mucor
+ 0.175460021426 0.182349699549 0.227217806440 0.247563133706 0.160750248794
+ 0.138031643786 0.000000000000 0.072991018602 0.271991858303 0.272704035853
+ 0.729075758693 0.676155341917 0.671334562854 0.699499598663 0.773928364495
+Absidia
+ 0.171381705808 0.164080100858 0.204178994811 0.219781287346 0.145644518755
+ 0.122675348331 0.072991018602 0.000000000000 0.261401901747 0.259659630766
+ 0.714834621911 0.648508655180 0.643308824691 0.676862516776 0.764373341245
+Arabidops
+ 0.242558390091 0.255776516678 0.256220603581 0.273666339087 0.280385638946
+ 0.273008128171 0.271991858303 0.261401901747 0.000000000000 0.031785685549
+ 0.750900038825 0.671512195407 0.693073592410 0.730190796496 0.792617210957
+Lycopersi
+ 0.239818426034 0.244680817390 0.255322597474 0.290368846607 0.278657537403
+ 0.278020382072 0.272704035853 0.259659630766 0.031785685549 0.000000000000
+ 0.745732191534 0.659295620612 0.674320313265 0.720433145071 0.789316205974
+Sulpholob
+ 0.711229145466 0.715551867177 0.719922660503 0.764658513106 0.733098885492
+ 0.713140264266 0.729075758693 0.714834621911 0.750900038825 0.745732191534
+ 0.000000000000 0.576508504143 0.604648603433 0.694265147576 0.741009725023
+Thermococ
+ 0.627975207365 0.644715916524 0.628402341913 0.661840294620 0.643129634435
+ 0.625663809960 0.676155341917 0.648508655180 0.671512195407 0.659295620612
+ 0.576508504143 0.000000000000 0.493086506111 0.523696929224 0.538544990613
+Thermopla
+ 0.657474744501 0.649699323398 0.635238587361 0.694883040771 0.664012590502
+ 0.657954595852 0.671334562854 0.643308824691 0.693073592410 0.674320313265
+ 0.604648603433 0.493086506111 0.000000000000 0.512104690742 0.559086291661
+Methanoco
+ 0.681818041556 0.692484941077 0.650765472456 0.665517479246 0.693115324686
+ 0.683280435752 0.699499598663 0.676862516776 0.730190796496 0.720433145071
+ 0.694265147576 0.523696929224 0.512104690742 0.000000000000 0.515261390739
+Halobacte
+ 0.738465099336 0.756225268778 0.728333862467 0.744690215581 0.754796557471
+ 0.745473130516 0.773928364495 0.764373341245 0.792617210957 0.789316205974
+ 0.741009725023 0.538544990613 0.559086291661 0.515261390739 0.000000000000
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.ml
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.ml (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.ml 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,150 @@
+protml 2.3b3 (11/09/01) JTT-F 15 OTUs 409 sites. test15.ptn
+#1
+ :-1 Homo
+ :--16
+ : :-2 Xenopus
+ :-18
+ : : :--3 Drosophil
+ : :--17
+ : :---4 Artemia
+ :---22
+ : : :--5 Saccharom
+ : : :--19
+ : : : :--6 Candida
+ : :--21
+ : : :--7 Mucor
+ : :--20
+ : :-8 Absidia
+:----------24
+: : :-9 Arabidops
+: :----23
+: :-10 Lycopersi
+:
+:------------11 Sulpholob
+:
+: :-------12 Thermococ
+:----27
+ : :---------13 Thermopla
+ :---26
+ : :---------14 Methanoco
+ :----25
+ :----------15 Halobacte
+
+No.1 ext. branch S.E. int. branch S.E.
+Homo 1 1.25 0.64 16 5.33 1.31
+Xenopus 2 2.52 0.84 17 6.10 1.39
+Drosophil 3 4.11 1.12 18 1.67 0.87
+Artemia 4 8.65 1.57 19 3.57 1.11
+Saccharom 5 5.45 1.29 20 4.99 1.30
+Candida 6 3.91 1.12 21 5.24 1.37
+Mucor 7 5.03 1.21 22 6.34 1.69
+Absidia 8 2.69 0.93 23 12.06 2.14
+Arabidops 9 2.07 0.76 24 29.94 3.79
+Lycopersi 10 1.17 0.60 25 10.56 2.30
+Sulpholob 11 37.09 4.11 26 6.32 2.10
+Thermococ 12 20.28 2.95 27 10.49 2.45
+Thermopla 13 25.06 3.19 TBL : 275.20 iter: 6
+Methanoco 14 25.01 3.27 ln L: -5932.72 +- 198.62
+Halobacte 15 28.29 3.46 AIC : 11957.43
+#2
+ :-1 Homo
+ :--16
+ : :-2 Xenopus
+ :-18
+ : : :--3 Drosophil
+ : :--17
+ : :---4 Artemia
+:------------24
+: : :--5 Saccharom
+: : :--19
+: : : :--6 Candida
+: : :--21
+: : : : :--7 Mucor
+: : : :--20
+: : : :-8 Absidia
+: :-23
+: : :-9 Arabidops
+: :------22
+: :-10 Lycopersi
+:
+:------------11 Sulpholob
+:
+: :-------12 Thermococ
+:----27
+ : :---------13 Thermopla
+ :---26
+ : :---------14 Methanoco
+ :----25
+ :----------15 Halobacte
+
+No.2 ext. branch S.E. int. branch S.E.
+Homo 1 1.28 0.65 16 5.37 1.32
+Xenopus 2 2.49 0.84 17 6.08 1.38
+Drosophil 3 4.10 1.12 18 2.05 0.96
+Artemia 4 8.63 1.57 19 3.25 1.07
+Saccharom 5 5.49 1.29 20 5.28 1.34
+Candida 6 3.88 1.12 21 5.37 1.40
+Mucor 7 4.97 1.20 22 18.00 2.41
+Absidia 8 2.78 0.95 23 lower limit
+Arabidops 9 2.01 0.75 24 35.20 4.06
+Lycopersi 10 1.23 0.60 25 10.46 2.29
+Sulpholob 11 37.25 4.13 26 6.28 2.10
+Thermococ 12 20.39 2.96 27 10.04 2.45
+Thermopla 13 25.25 3.20 TBL : 280.52 iter: 6
+Methanoco 14 25.15 3.28 ln L: -5949.46 +- 199.28
+Halobacte 15 28.24 3.46 AIC : 11990.92 lower limit: 0.001
+#3
+ :-1 Homo
+ :--16
+ : :-2 Xenopus
+ :-18
+ : : :--3 Drosophil
+ : :--17
+ : :---4 Artemia
+ :--20
+ : : :-9 Arabidops
+ : :------19
+ : :-10 Lycopersi
+:------------24
+: : :--5 Saccharom
+: : :--21
+: : : :--6 Candida
+: :-23
+: : :--7 Mucor
+: :--22
+: :-8 Absidia
+:
+:------------11 Sulpholob
+:
+: :-------12 Thermococ
+:----27
+ : :---------13 Thermopla
+ :---26
+ : :---------14 Methanoco
+ :----25
+ :----------15 Halobacte
+
+No.3 ext. branch S.E. int. branch S.E.
+Homo 1 1.24 0.63 16 5.56 1.34
+Xenopus 2 2.52 0.84 17 5.84 1.36
+Drosophil 3 4.11 1.12 18 1.54 0.89
+Artemia 4 8.64 1.57 19 17.51 2.37
+Saccharom 5 5.57 1.30 20 3.20 1.23
+Candida 6 3.81 1.11 21 3.22 1.07
+Mucor 7 5.08 1.21 22 5.23 1.33
+Absidia 8 2.67 0.92 23 2.86 1.17
+Arabidops 9 2.01 0.74 24 34.39 3.99
+Lycopersi 10 1.23 0.60 25 10.32 2.28
+Sulpholob 11 36.97 4.13 26 6.60 2.17
+Thermococ 12 20.34 2.97 27 9.94 2.43
+Thermopla 13 25.27 3.21 TBL : 279.10 iter: 6
+Methanoco 14 25.14 3.28 ln L: -5943.64 +- 199.09
+Halobacte 15 28.29 3.46 AIC : 11979.29
+
+protml 2.3b3 JTT-F 3 trees 15 OTUs 409 sites. test15.ptn
+
+Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL
+-----------------------------------------------------------
+1 -5932.7 0.0 <-best 46 11957.4 0.0 ME
+2 -5949.5 -16.7 7.8 46 11990.9 33.5 5.3
+3 -5943.6 -10.9 9.2 46 11979.3 21.9 3.9
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.nj
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.nj (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.nj 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,31 @@
+njdist 1.2.5 (11/09/01) 15 OTUs 409 sites JTT test15.ptn
+
+ :-1 Homo
+ :--21
+ : :-2 Xenopus
+ :-27
+ : : :--3 Drosophil
+ : :--22
+ : :---4 Artemia
+ :-26
+ : : :--5 Saccharom
+ : : :-24
+ : : : :--6 Candida
+ : :--25
+ : : :--7 Mucor
+ : :--23
+ : :-8 Absidia
+ :----------19
+ : : :-9 Arabidops
+ : :-----20
+ : :-10 Lycopersi
+ :-18
+ : :------------11 Sulpholob
+ :-17
+ : :--------12 Thermococ
+:--16
+: :--------13 Thermopla
+:
+:--------14 Methanoco
+:
+:----------15 Halobacte
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.nj-2.2
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.nj-2.2 (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.nj-2.2 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,33 @@
+njdist 1.2.1 Jul 2 1994 15 OTUs 409 sites JTT test15.ptn
+
+ :-1 Homo
+:--21
+: :-2 Xenopus
+:
+: :--3 Drosophil
+:--22
+: :---4 Artemia
+:
+: :--5 Saccharom
+: :-24
+: : :--6 Candida
+: :--25
+: : : :--7 Mucor
+: : :--23
+: : :-8 Absidia
+:-27
+ : :-9 Arabidops
+ : :-----20
+ : : :-10 Lycopersi
+ :-26
+ : :------------11 Sulpholob
+ :----------19
+ : :--------12 Thermococ
+ :-18
+ : :--------13 Thermopla
+ :-17
+ : :--------14 Methanoco
+ :--16
+ :----------15 Halobacte
+
+((Homo,Xenopus),(Drosophil,Artemia),(((Saccharom,Candida),(Mucor,Absidia)),((Arabidops,Lycopersi),(Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))))));
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.njo
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.njo (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.njo 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,31 @@
+njdist 1.2.5 (11/09/01) 15 OTUs 409 sites JTT test15.ptn
+
+ :-1 Homo
+ :--21
+ : :-2 Xenopus
+ :-27
+ : : :--3 Drosophil
+ : :--22
+ : :---4 Artemia
+ :-26
+ : : :--5 Saccharom
+ : : :-24
+ : : : :--6 Candida
+ : :--25
+ : : :--7 Mucor
+ : :--23
+ : :-8 Absidia
+:----------19
+: : :-9 Arabidops
+: :-----20
+: :-10 Lycopersi
+:
+:------------11 Sulpholob
+:
+: :--------12 Thermococ
+:-18
+ : :--------13 Thermopla
+ :-17
+ : :--------14 Methanoco
+ :--16
+ :----------15 Halobacte
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.tpl
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.tpl (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.tpl 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,29 @@
+3 / 3 protml 2.3b3 "JTT-F" 15 OTUs 409 sites. test15.ptn
+# <= 105 trees (top ranking for approx. ln L) in the top 200.0% range of TBL
+# range TBL trees
+# < 247.49 0
+# 5% 256.06 3 **************************************************
+# 10% 264.64 0
+# 15% 273.22 0
+# 20% 281.80 0
+# 25% 290.38 0
+# 30% 298.96 0
+# 35% 307.54 0
+# 40% 316.12 0
+# 45% 324.69 0
+# 50% 333.27 0
+# 55% 341.85 0
+# 60% 350.43 0
+# 65% 359.01 0
+# 70% 367.59 0
+# 75% 376.17 0
+# 80% 384.74 0
+# 85% 393.32 0
+# 90% 401.90 0
+# 95% 410.48 0
+# 100% 419.06 0
+# over 0
+# approx. ln L -5967.7 ... -5979.3 diff 11.5, TBL 247.5 ... 248.3 diff 0.8
+(((((Homo,Xenopus),(Drosophil,Artemia)),((Saccharom,Candida),(Mucor,Absidia))),(Arabidops,Lycopersi)),Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))); 0.0
+((((Homo,Xenopus),(Drosophil,Artemia)),(((Saccharom,Candida),(Mucor,Absidia)),(Arabidops,Lycopersi))),Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))); 10.7
+(((((Homo,Xenopus),(Drosophil,Artemia)),(Arabidops,Lycopersi)),((Saccharom,Candida),(Mucor,Absidia))),Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))); 11.5
Added: trunk/packages/molphy/trunk/debian/tests/compare/test15.tree
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test15.tree (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test15.tree 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,5 @@
+(((((Homo:1.456,Xenopus:2.215):5.159,(Drosophil:5.257,Artemia:7.247):3.724)
+:1.075,((Saccharom:5.073,Candida:4.014):2.615,(Mucor:4.444,Absidia:2.810)
+:3.308):3.309):1.947,(Arabidops:1.604,Lycopersi:1.554):12.729):26.645,
+Sulpholob:33.726,(Thermococ:23.040,(Thermopla:23.538,(Methanoco:22.576,
+Halobacte:28.715):4.132):1.271):2.403);
Added: trunk/packages/molphy/trunk/debian/tests/compare/test4.dis
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test4.dis (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test4.dis 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,9 @@
+4 90 sites JTT test4.ptn
+Data1
+ 0.000000000000 0.253161436877 0.204206481653 0.228541838813
+Data2
+ 0.253161436877 0.000000000000 0.167720557577 0.253821429711
+Data3
+ 0.204206481653 0.167720557577 0.000000000000 0.218809727904
+Data4
+ 0.228541838813 0.253821429711 0.218809727904 0.000000000000
Added: trunk/packages/molphy/trunk/debian/tests/compare/test4.ml
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test4.ml (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test4.ml 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,51 @@
+protml 2.3b3 (11/09/01) JTT 4 OTUs 90 sites. test4.ptn
+#1
+:------------1 Data1
+:
+: :------------2 Data2
+:--------5
+: :------3 Data3
+:
+:------------4 Data4
+
+No.1 ext. branch S.E. int. branch S.E.
+Data1 1 11.72 4.07 5 6.01 3.04
+Data2 2 11.42 3.95 TBL : 46.07 iter: 5
+Data3 3 5.37 2.81 ln L: -461.51 +- 27.47
+Data4 4 11.55 4.14 AIC : 933.01
+#2
+:----------------1 Data1
+:
+:-------------2 Data2
+:
+: :-----------------4 Data4
+:--5
+ :-------3 Data3
+
+No.2 ext. branch S.E. int. branch S.E.
+Data1 1 15.42 4.70 5 lower limit
+Data2 2 12.07 4.15 TBL : 50.35 iter: 5
+Data3 3 6.63 3.18 ln L: -467.27 +- 27.92
+Data4 4 16.23 4.83 AIC : 944.55 lower limit: 0.001
+#3
+ :----------------1 Data1
+:----5
+: :------3 Data3
+:
+:-----------2 Data2
+:
+:---------------4 Data4
+
+No.3 ext. branch S.E. int. branch S.E.
+Data1 1 15.11 4.60 5 2.77 2.25
+Data2 2 10.41 3.90 TBL : 48.85 iter: 6
+Data3 3 5.75 2.96 ln L: -465.53 +- 27.68
+Data4 4 14.80 4.61 AIC : 941.07
+
+protml 2.3b3 JTT 3 trees 4 OTUs 90 sites. test4.ptn
+
+Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL RELL-BP
+-------------------------------------------------------------------
+1 -461.5 0.0 <-best 5 933.0 0.0 ME 0.7772
+2 -467.3 -5.8 4.3 5 944.5 11.5 4.3 0.0087
+3 -465.5 -4.0 5.3 5 941.1 8.1 2.8 0.2141
Added: trunk/packages/molphy/trunk/debian/tests/compare/test4.nj
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test4.nj (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test4.nj 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,9 @@
+njdist 1.2.5 (11/09/01) 4 OTUs 90 sites JTT test4.ptn
+
+:------------1 Data1
+:
+: :-----------2 Data2
+:-----5
+: :-------3 Data3
+:
+:------------4 Data4
Added: trunk/packages/molphy/trunk/debian/tests/compare/test4.nj-2.2
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test4.nj-2.2 (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test4.nj-2.2 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,11 @@
+njdist 1.2.1 Jul 2 1994 4 OTUs 90 sites JTT test4.ptn
+
+ :-----------1 Data1
+:-----5
+: :------------4 Data4
+:
+:-----------2 Data2
+:
+:-------3 Data3
+
+((Data1,Data4),Data2,Data3);
Added: trunk/packages/molphy/trunk/debian/tests/compare/test4.tpl
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test4.tpl (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test4.tpl 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,29 @@
+3 / 3 protml 2.3b3 "JTT" 4 OTUs 90 sites. test4.ptn
+# <= 105 trees (top ranking for approx. ln L) in the top 200.0% range of TBL
+# range TBL trees
+# < 43.06 0
+# 5% 43.16 1 **************************************************
+# 10% 43.25 0
+# 15% 43.35 0
+# 20% 43.44 0
+# 25% 43.54 0
+# 30% 43.63 0
+# 35% 43.73 0
+# 40% 43.82 0
+# 45% 43.91 0
+# 50% 44.01 0
+# 55% 44.10 0
+# 60% 44.20 0
+# 65% 44.29 0
+# 70% 44.39 0
+# 75% 44.48 0
+# 80% 44.58 0
+# 85% 44.67 1 **************************************************
+# 90% 44.77 0
+# 95% 44.86 0
+# 100% 44.96 1 **************************************************
+# over 0
+# approx. ln L -462.1 ... -467.7 diff 5.6, TBL 43.1 ... 44.6 diff 1.5
+(Data1,(Data2,Data3),Data4); 0.0
+(Data1,Data2,(Data4,Data3)); 5.6
+((Data1,Data3),Data2,Data4); 5.6
Added: trunk/packages/molphy/trunk/debian/tests/compare/test5.ml
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test5.ml (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test5.ml 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,276 @@
+protml 2.3b3 (11/09/01) JTT 5 OTUs 352 sites. test5.ptn
+#1
+:----------1 Tabac_chl
+:
+:------4 Fremyella
+:
+: :-----------------5 Synechocy
+:---7
+ : :-------2 Prochloro
+ :----6
+ :--3 Anacystis
+
+No.1 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.38 1.76 6 2.28 0.92
+Prochloro 2 6.25 1.41 7 1.14 0.69
+Anacystis 3 1.50 0.74 TBL : 42.19 iter: 5
+Fremyella 4 5.43 1.34 ln L: -1793.14 +- 65.40
+Synechocy 5 16.21 2.36 AIC : 3600.27
+#2
+ :----------1 Tabac_chl
+:--7
+: : :-------2 Prochloro
+: :----6
+: :--3 Anacystis
+:
+:------4 Fremyella
+:
+:----------------5 Synechocy
+
+No.2 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.78 1.80 6 2.57 0.99
+Prochloro 2 6.36 1.42 7 0.97 0.73
+Anacystis 3 1.43 0.74 TBL : 42.43 iter: 5
+Fremyella 4 5.34 1.36 ln L: -1796.92 +- 66.12
+Synechocy 5 15.98 2.36 AIC : 3607.84
+#3
+:----------1 Tabac_chl
+:
+: :-------4 Fremyella
+:--7
+: : :-------2 Prochloro
+: :----6
+: :--3 Anacystis
+:
+:-----------------5 Synechocy
+
+No.3 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.28 1.79 6 2.63 1.01
+Prochloro 2 6.35 1.42 7 0.91 0.80
+Anacystis 3 1.44 0.74 TBL : 42.74 iter: 6
+Fremyella 4 6.02 1.42 ln L: -1797.75 +- 65.83
+Synechocy 5 16.10 2.38 AIC : 3609.51
+#4
+:----------1 Tabac_chl
+:
+:------4 Fremyella
+:
+: :-------------------5 Synechocy
+: :--6
+: : :--3 Anacystis
+:----7
+ :-------2 Prochloro
+
+No.4 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.46 1.75 6 lower limit
+Prochloro 2 6.43 1.45 7 2.74 1.04
+Anacystis 3 1.89 0.86 TBL : 44.09 iter: 6
+Fremyella 4 5.50 1.35 ln L: -1804.43 +- 65.88
+Synechocy 5 18.08 2.49 AIC : 3622.87 lower limit: 0.001
+#5
+:----------1 Tabac_chl
+:
+:------4 Fremyella
+:
+: :------------------5 Synechocy
+: :---6
+: : :------2 Prochloro
+:----7
+ :--3 Anacystis
+
+No.5 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.36 1.74 6 1.25 0.75
+Prochloro 2 5.31 1.35 7 2.74 1.03
+Anacystis 3 1.66 0.81 TBL : 43.00 iter: 6
+Fremyella 4 5.52 1.35 ln L: -1799.81 +- 65.48
+Synechocy 5 17.15 2.43 AIC : 3613.63
+#6
+ :------------1 Tabac_chl
+ :--6
+ : :--3 Anacystis
+:----7
+: :-------2 Prochloro
+:
+:------4 Fremyella
+:
+:----------------5 Synechocy
+
+No.6 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 11.31 1.94 6 0.57 0.54
+Prochloro 2 6.10 1.44 7 2.61 1.09
+Anacystis 3 1.92 0.87 TBL : 43.48 iter: 6
+Fremyella 4 5.32 1.36 ln L: -1808.97 +- 66.86
+Synechocy 5 15.65 2.33 AIC : 3631.94
+#7
+ :-----------1 Tabac_chl
+ :---6
+ : :------2 Prochloro
+:----7
+: :--3 Anacystis
+:
+:------4 Fremyella
+:
+:----------------5 Synechocy
+
+No.7 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 10.46 1.87 6 1.42 0.75
+Prochloro 2 5.22 1.36 7 2.70 1.10
+Anacystis 3 1.90 0.86 TBL : 42.94 iter: 6
+Fremyella 4 5.47 1.38 ln L: -1803.71 +- 66.47
+Synechocy 5 15.76 2.34 AIC : 3621.43
+#8
+ :----------1 Tabac_chl
+:---6
+: :-------2 Prochloro
+:
+:-------4 Fremyella
+:
+: :------------------5 Synechocy
+:--7
+ :---3 Anacystis
+
+No.8 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.72 1.79 6 1.41 0.75
+Prochloro 2 6.10 1.46 7 lower limit
+Anacystis 3 2.88 1.01 TBL : 44.17 iter: 5
+Fremyella 4 6.95 1.51 ln L: -1810.28 +- 66.73
+Synechocy 5 17.11 2.42 AIC : 3634.55 lower limit: 0.001
+#9
+:----------1 Tabac_chl
+:
+: :--------4 Fremyella
+: :--6
+: : :-------2 Prochloro
+:----7
+: :---3 Anacystis
+:
+:-----------------5 Synechocy
+
+No.9 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.23 1.79 6 0.56 0.55
+Prochloro 2 6.48 1.48 7 2.31 1.09
+Anacystis 3 2.19 0.93 TBL : 44.01 iter: 7
+Fremyella 4 7.22 1.56 ln L: -1811.22 +- 66.41
+Synechocy 5 16.01 2.36 AIC : 3636.44
+#10
+ :-----------1 Tabac_chl
+:--6
+: :---3 Anacystis
+:
+:-------4 Fremyella
+:
+: :-----------------5 Synechocy
+:---7
+ :-------2 Prochloro
+
+No.10 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 10.42 1.84 6 0.40 0.50
+Prochloro 2 6.13 1.45 7 1.22 0.75
+Anacystis 3 2.75 0.98 TBL : 43.67 iter: 5
+Fremyella 4 6.67 1.48 ln L: -1810.93 +- 66.72
+Synechocy 5 16.08 2.35 AIC : 3635.87
+#11
+ :----------1 Tabac_chl
+:---6
+: :-------2 Prochloro
+:
+: :-------4 Fremyella
+:--7
+: :---3 Anacystis
+:
+:------------------5 Synechocy
+
+No.11 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.72 1.79 6 1.41 0.75
+Prochloro 2 6.10 1.46 7 lower limit
+Anacystis 3 2.88 1.01 TBL : 44.17 iter: 5
+Fremyella 4 6.95 1.51 ln L: -1810.28 +- 66.73
+Synechocy 5 17.11 2.42 AIC : 3634.56 lower limit: 0.001
+#12
+ :-----------1 Tabac_chl
+:--6
+: :---3 Anacystis
+:
+: :-------4 Fremyella
+:--7
+: :--------2 Prochloro
+:
+:-----------------5 Synechocy
+
+No.12 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 10.56 1.85 6 0.31 0.46
+Prochloro 2 7.03 1.52 7 0.43 0.50
+Anacystis 3 2.74 0.97 TBL : 44.63 iter: 6
+Fremyella 4 6.59 1.48 ln L: -1814.74 +- 67.02
+Synechocy 5 16.97 2.42 AIC : 3643.48
+#13
+:-----------1 Tabac_chl
+:
+: :-------4 Fremyella
+:--6
+: :---3 Anacystis
+:
+: :-----------------5 Synechocy
+:---7
+ :-------2 Prochloro
+
+No.13 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 10.44 1.84 6 0.02 0.45
+Prochloro 2 6.24 1.46 7 1.39 0.78
+Anacystis 3 2.83 0.99 TBL : 43.86 iter: 7
+Fremyella 4 6.85 1.49 ln L: -1811.42 +- 66.77
+Synechocy 5 16.09 2.35 AIC : 3636.84
+#14
+:-----------1 Tabac_chl
+:
+: :-------4 Fremyella
+:--6
+: :--------2 Prochloro
+:
+: :------------------5 Synechocy
+:--7
+ :---3 Anacystis
+
+No.14 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 10.62 1.86 6 0.56 0.54
+Prochloro 2 7.14 1.53 7 lower limit
+Anacystis 3 2.84 0.99 TBL : 44.87 iter: 5
+Fremyella 4 6.56 1.47 ln L: -1815.13 +- 67.02
+Synechocy 5 17.15 2.43 AIC : 3644.26 lower limit: 0.001
+#15
+:----------1 Tabac_chl
+:
+: :--------4 Fremyella
+: :--6
+: : :---3 Anacystis
+:----7
+: :-------2 Prochloro
+:
+:-----------------5 Synechocy
+
+No.15 ext. branch S.E. int. branch S.E.
+Tabac_chl 1 9.20 1.79 6 0.09 0.50
+Prochloro 2 6.74 1.51 7 2.34 1.10
+Anacystis 3 2.32 0.95 TBL : 44.27 iter: 7
+Fremyella 4 7.57 1.59 ln L: -1812.58 +- 66.59
+Synechocy 5 16.01 2.36 AIC : 3639.16
+
+protml 2.3b3 JTT 15 trees 5 OTUs 352 sites. test5.ptn
+
+Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL
+-----------------------------------------------------------
+1 -1793.1 0.0 <-best 7 3600.3 0.0 ME
+2 -1796.9 -3.8 6.0 7 3607.8 7.6 0.2
+3 -1797.8 -4.6 5.6 7 3609.5 9.2 0.5
+4 -1804.4 -11.3 6.4 7 3622.9 22.6 1.9
+5 -1799.8 -6.7 8.1 7 3613.6 13.4 0.8
+6 -1809.0 -15.8 10.0 7 3631.9 31.7 1.3
+7 -1803.7 -10.6 11.4 7 3621.4 21.2 0.7
+8 -1810.3 -17.1 11.8 7 3634.6 34.3 2.0
+9 -1811.2 -18.1 10.3 7 3636.4 36.2 1.8
+10 -1810.9 -17.8 11.5 7 3635.9 35.6 1.5
+11 -1810.3 -17.1 11.8 7 3634.6 34.3 2.0
+12 -1814.7 -21.6 10.7 7 3643.5 43.2 2.4
+13 -1811.4 -18.3 11.4 7 3636.8 36.6 1.7
+14 -1815.1 -22.0 10.6 7 3644.3 44.0 2.7
+15 -1812.6 -19.4 9.8 7 3639.2 38.9 2.1
Added: trunk/packages/molphy/trunk/debian/tests/compare/test5.nj
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test5.nj (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test5.nj 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,18 @@
+njdist 1.2.5 (11/09/01) 5 OTUs 352 sites JTT test5.ptn
+
+ :---------1 Tabac_chl
+:--7
+: : :------2 Prochloro
+: :---6
+: :---3 Anacystis
+:
+:------4 Fremyella
+:
+:---------------5 Synechocy
+
+ num length num length
+Tabac_chl 1 8.91 6 1.24
+Prochloro 2 5.17 7 0.63
+Anacystis 3 2.55
+Fremyella 4 5.41
+Synechocy 5 14.94
Added: trunk/packages/molphy/trunk/debian/tests/compare/test5.tpl
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test5.tpl (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test5.tpl 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,41 @@
+15 / 15 protml 2.3b3 "JTT" 5 OTUs 352 sites. test5.ptn
+# <= 105 trees (top ranking for approx. ln L) in the top 200.0% range of TBL
+# range TBL trees
+# < 38.85 0
+# 5% 38.94 1 ************
+# 10% 39.03 0
+# 15% 39.12 1 ************
+# 20% 39.21 0
+# 25% 39.30 1 ************
+# 30% 39.39 0
+# 35% 39.48 1 ************
+# 40% 39.57 1 ************
+# 45% 39.66 1 ************
+# 50% 39.75 0
+# 55% 39.84 0
+# 60% 39.93 4 **************************************************
+# 65% 40.02 1 ************
+# 70% 40.11 0
+# 75% 40.20 1 ************
+# 80% 40.29 0
+# 85% 40.38 1 ************
+# 90% 40.47 1 ************
+# 95% 40.56 0
+# 100% 40.65 1 ************
+# over 0
+# approx. ln L -1798.8 ... -1818.0 diff 19.1, TBL 39.0 ... 39.9 diff 0.9
+(Tabac_chl,Fremyella,(Synechocy,(Prochloro,Anacystis))); 0.0
+((Tabac_chl,(Prochloro,Anacystis)),Fremyella,Synechocy); 0.9
+(Tabac_chl,(Fremyella,(Prochloro,Anacystis)),Synechocy); 1.9
+(Tabac_chl,Fremyella,((Synechocy,Anacystis),Prochloro)); 9.3
+(Tabac_chl,Fremyella,((Synechocy,Prochloro),Anacystis)); 10.2
+(((Tabac_chl,Anacystis),Prochloro),Fremyella,Synechocy); 13.6
+(((Tabac_chl,Prochloro),Anacystis),Fremyella,Synechocy); 13.6
+((Tabac_chl,Prochloro),Fremyella,(Synechocy,Anacystis)); 14.4
+(Tabac_chl,((Fremyella,Prochloro),Anacystis),Synechocy); 16.7
+((Tabac_chl,Anacystis),Fremyella,(Synechocy,Prochloro)); 16.7
+((Tabac_chl,Prochloro),(Fremyella,Anacystis),Synechocy); 17.6
+((Tabac_chl,Anacystis),(Fremyella,Prochloro),Synechocy); 17.9
+(Tabac_chl,(Fremyella,Anacystis),(Synechocy,Prochloro)); 18.0
+(Tabac_chl,(Fremyella,Prochloro),(Synechocy,Anacystis)); 18.5
+(Tabac_chl,((Fremyella,Anacystis),Prochloro),Synechocy); 19.1
Added: trunk/packages/molphy/trunk/debian/tests/compare/test6.ml
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test6.ml (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test6.ml 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,216 @@
+nucml 2.3b3 (11/09/01) A/B:30.58 F 6 OTUs 1344 sites. test6.nuc
+#1
+ :--1 Chimp
+ :---7
+ : :-2 Bonobo
+ :---8
+ : :-----3 Human
+:-----9
+: :-----4 Gorilla
+:
+:----------5 Orang
+:
+:----------------6 Siamang
+
+No.1 ext. branch S.E. int. branch S.E.
+Chimp 1 6.55 0.93 7 9.54 1.76
+Bonobo 2 4.06 0.83 8 9.50 2.21
+Human 3 20.07 2.12 9 16.61 3.96
+Gorilla 4 20.98 2.60 TBL : 213.70 iter: 7
+Orang 5 47.78 5.82 ln L: -5539.83 +- 79.93
+Siamang 6 78.61 8.58 AIC : 11105.67
+#2
+ :--1 Chimp
+ :---7
+ : :-2 Bonobo
+:---8
+: :-----3 Human
+:
+: :-------------5 Orang
+:--9
+: :-----4 Gorilla
+:
+:--------------------6 Siamang
+
+No.2 ext. branch S.E. int. branch S.E.
+Chimp 1 6.57 0.94 7 9.47 1.76
+Bonobo 2 4.04 0.83 8 8.98 2.17
+Human 3 20.11 2.12 9 1.75 1.58
+Gorilla 4 20.05 2.59 TBL : 230.46 iter: 8
+Orang 5 63.98 6.32 ln L: -5555.52 +- 80.45
+Siamang 6 95.51 9.43 AIC : 11137.04
+#3
+ :--1 Chimp
+ :----7
+ : :-2 Bonobo
+:------9
+: : :-----3 Human
+: :--8
+: :------4 Gorilla
+:
+:----------5 Orang
+:
+:----------------6 Siamang
+
+No.3 ext. branch S.E. int. branch S.E.
+Chimp 1 6.58 0.94 7 10.37 1.81
+Bonobo 2 4.02 0.83 8 lower limit
+Human 3 20.17 2.15 9 23.47 4.64
+Gorilla 4 29.43 2.77 TBL : 219.77 iter: 7
+Orang 5 47.88 6.03 ln L: -5559.12 +- 81.31
+Siamang 6 77.86 8.64 AIC : 11144.23 lower limit: 0.001
+#4
+ :--1 Chimp
+ :----7
+ : :-2 Bonobo
+ :--8
+ : :------4 Gorilla
+:------9
+: :-----3 Human
+:
+:----------5 Orang
+:
+:----------------6 Siamang
+
+No.4 ext. branch S.E. int. branch S.E.
+Chimp 1 6.58 0.94 7 10.37 1.81
+Bonobo 2 4.02 0.83 8 lower limit
+Human 3 20.17 2.15 9 23.47 4.64
+Gorilla 4 29.43 2.77 TBL : 219.77 iter: 7
+Orang 5 47.88 6.03 ln L: -5559.12 +- 81.31
+Siamang 6 77.86 8.64 AIC : 11144.23 lower limit: 0.001
+#5
+ :--1 Chimp
+ :---7
+ : :-2 Bonobo
+:---8
+: :-----3 Human
+:
+:-------------5 Orang
+:
+: :--------------------6 Siamang
+:--9
+ :-----4 Gorilla
+
+No.5 ext. branch S.E. int. branch S.E.
+Chimp 1 6.56 0.93 7 9.52 1.76
+Bonobo 2 4.05 0.83 8 9.82 2.23
+Human 3 20.07 2.12 9 lower limit
+Gorilla 4 20.94 2.61 TBL : 231.52 iter: 7
+Orang 5 64.53 6.39 ln L: -5556.18 +- 80.47
+Siamang 6 96.03 9.48 AIC : 11138.37 lower limit: 0.001
+#6
+ :--1 Chimp
+:---7
+: :-2 Bonobo
+:
+: :-------------5 Orang
+: :---8
+: : :-----4 Gorilla
+:--9
+: :-----3 Human
+:
+:---------------------6 Siamang
+
+No.6 ext. branch S.E. int. branch S.E.
+Chimp 1 6.63 0.94 7 8.46 1.78
+Bonobo 2 3.97 0.83 8 9.88 2.29
+Human 3 20.10 2.14 9 1.52 1.52
+Gorilla 4 20.18 2.58 TBL : 239.04 iter: 14
+Orang 5 64.30 6.35 ln L: -5571.97 +- 81.57
+Siamang 6 103.99 10.17 AIC : 11169.93
+#7
+ :--1 Chimp
+:---7
+: :-2 Bonobo
+:
+: :-------------5 Orang
+:---8
+: :-----4 Gorilla
+:
+: :---------------------6 Siamang
+:--9
+ :-----3 Human
+
+No.7 ext. branch S.E. int. branch S.E.
+Chimp 1 6.61 0.94 7 9.90 1.80
+Bonobo 2 4.00 0.83 8 9.85 2.29
+Human 3 20.22 2.15 9 lower limit
+Gorilla 4 20.20 2.58 TBL : 239.75 iter: 9
+Orang 5 64.34 6.35 ln L: -5572.27 +- 81.55
+Siamang 6 104.63 10.20 AIC : 11170.54 lower limit: 0.001
+#8
+ :--1 Chimp
+:----7
+: :-2 Bonobo
+:
+: :---------------5 Orang
+:--9
+: : :-----3 Human
+: :--8
+: :------4 Gorilla
+:
+:---------------------6 Siamang
+
+No.8 ext. branch S.E. int. branch S.E.
+Chimp 1 6.63 0.94 7 10.72 1.88
+Bonobo 2 3.95 0.83 8 lower limit
+Human 3 20.53 2.21 9 0.64 1.29
+Gorilla 4 28.35 2.71 TBL : 241.75 iter: 9
+Orang 5 70.17 6.83 ln L: -5584.22 +- 82.66
+Siamang 6 100.76 9.87 AIC : 11194.43 lower limit: 0.001
+#9
+ :--1 Chimp
+:----7
+: :-2 Bonobo
+:
+: :---------------5 Orang
+:--8
+: :----3 Human
+:
+: :--------------------6 Siamang
+:---9
+ :-----4 Gorilla
+
+No.9 ext. branch S.E. int. branch S.E.
+Chimp 1 6.58 0.94 7 10.33 1.82
+Bonobo 2 4.01 0.83 8 1.60 1.67
+Human 3 18.65 2.15 9 6.94 2.23
+Gorilla 4 22.47 2.66 TBL : 238.62 iter: 12
+Orang 5 71.52 7.02 ln L: -5579.67 +- 82.13
+Siamang 6 96.51 9.54 AIC : 11185.34
+#10
+ :--1 Chimp
+:----7
+: :-2 Bonobo
+:
+: :--------------5 Orang
+: :--8
+: : :----3 Human
+:--9
+: :------4 Gorilla
+:
+:---------------------6 Siamang
+
+No.10 ext. branch S.E. int. branch S.E.
+Chimp 1 6.64 0.94 7 10.64 1.87
+Bonobo 2 3.94 0.83 8 1.05 1.50
+Human 3 19.55 2.20 9 0.60 1.28
+Gorilla 4 28.39 2.72 TBL : 241.38 iter: 9
+Orang 5 69.75 6.82 ln L: -5584.00 +- 82.68
+Siamang 6 100.81 9.88 AIC : 11194.01
+
+nucml 2.3b3 A/B:30.58 F 10 trees 6 OTUs 1344 sites. test6.nuc
+
+Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL
+-----------------------------------------------------------
+1 -5539.8 0.0 <-best 13 11105.7 0.0 ME
+2 -5555.5 -15.7 7.0 13 11137.0 31.4 16.8
+3 -5559.1 -19.3 8.2 13 11144.2 38.6 6.1
+4 -5559.1 -19.3 8.2 13 11144.2 38.6 6.1
+5 -5556.2 -16.3 6.8 13 11138.4 32.7 17.8
+6 -5572.0 -32.1 10.7 13 11169.9 64.3 25.3
+7 -5572.3 -32.4 10.5 13 11170.5 64.9 26.0
+8 -5584.2 -44.4 13.1 13 11194.4 88.8 28.1
+9 -5579.7 -39.8 11.2 13 11185.3 79.7 24.9
+10 -5584.0 -44.2 13.2 13 11194.0 88.3 27.7
Added: trunk/packages/molphy/trunk/debian/tests/compare/test6.mlq
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test6.mlq (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test6.mlq 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,22 @@
+nucml 2.3b3 (11/09/01) A/B:opt F 6 OTUs 1344 sites. test6.nuc
+#1
+Alpha/Beta: 30.987
+ :----1 Chimp
+ :------7
+ : :--2 Bonobo
+ :------8
+ : :----------3 Human
+:---------9
+: :----------4 Gorilla
+:
+:-----------------------5 Orang
+:
+:--------------------------------------6 Siamang
+
+No.1 ext. branch S.E. int. branch S.E.
+Chimp 1 6.56 0.94 7 9.55 1.76
+Bonobo 2 4.06 0.83 8 9.53 2.22
+Human 3 20.09 2.13 9 16.70 3.99
+Gorilla 4 21.01 2.61 TBL : 214.99 iter: 9
+Orang 5 48.11 5.88 ln L: -5539.83 +- 79.97
+Siamang 6 79.39 8.71 AIC : 11105.65
Added: trunk/packages/molphy/trunk/debian/tests/compare/test6.mls
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test6.mls (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test6.mls 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,45 @@
+nucml 2.3b3 (11/09/01) A/B:4.00 F 6 OTUs 1344 sites. test6.nuc
+#0
+:----1 Chimp
+:
+:---2 Bonobo
+:
+:-----------3 Human
+:
+:-------------4 Gorilla
+:
+:--------------------5 Orang
+:
+:------------------------6 Siamang
+#1
+ :---1 Chimp
+:------7
+: :--2 Bonobo
+:
+:--------3 Human
+:
+:----------4 Gorilla
+:
+: :------------5 Orang
+:--------8
+ :-----------------6 Siamang
+
+ :---1 Chimp
+ :-----7
+ : :--2 Bonobo
+ :----9
+ : :--------3 Human
+:-------8
+: :--------4 Gorilla
+:
+:------------5 Orang
+:
+:-----------------6 Siamang
+
+No.1 ext. branch S.E. int. branch S.E.
+Chimp 1 6.01 0.81 7 8.31 1.19
+Bonobo 2 3.95 0.71 8 11.59 1.82
+Human 3 16.01 1.46 9 6.04 1.29
+Gorilla 4 17.01 1.61 TBL : 128.72 iter: 7
+Orang 5 24.67 2.18 ln L: -5889.71 +- 80.88
+Siamang 6 35.12 2.57 AIC : 11805.42
Added: trunk/packages/molphy/trunk/debian/tests/compare/test6.mls-2.2
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test6.mls-2.2 (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test6.mls-2.2 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,25 @@
+nucml 2.2 Jul 2 1994 A/B:4.00 F 6 OTUs 1344 sites test6.nuc
+
+((Chimp,Bonobo),Human,Gorilla,Orang,Siamang);
+((Chimp,Bonobo),Human,Gorilla,(Orang,Siamang));
+(((Chimp,Bonobo),Human),Gorilla,(Orang,Siamang));
+
+ :---1 Chimp
+ :-----7
+ : :--2 Bonobo
+:----9
+: :--------3 Human
+:
+:--------4 Gorilla
+:
+: :------------5 Orang
+:-------8
+ :-----------------6 Siamang
+
+No.1 num length S.E. num length S.E.
+Chimp 1 5.96 0.80 7 8.23 1.18
+Bonobo 2 3.91 0.70 8 11.49 1.81
+Human 3 15.88 1.45 9 6.00 1.28
+Gorilla 4 16.87 1.60 6
+Orang 5 24.48 2.17 ln L: -5886.55 +- 80.83
+Siamang 6 34.86 2.55 AIC : 11799.10
Added: trunk/packages/molphy/trunk/debian/tests/compare/test6.tpl
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test6.tpl (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test6.tpl 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,36 @@
+10 / 105 nucml 2.3b3 "A/B:30.58 F" 6 OTUs 1344 sites. test6.nuc
+# <= 10 trees (top ranking for approx. ln L) in the top 200.0% range of TBL
+# range TBL trees
+# < 216.29 0
+# 5% 217.80 1 ***
+# 10% 219.31 2 *******
+# 15% 220.82 0
+# 20% 222.33 2 *******
+# 25% 223.84 1 ***
+# 30% 225.35 3 **********
+# 35% 226.86 7 *************************
+# 40% 228.37 7 *************************
+# 45% 229.88 5 *****************
+# 50% 231.39 1 ***
+# 55% 232.90 3 **********
+# 60% 234.41 4 **************
+# 65% 235.92 7 *************************
+# 70% 237.43 14 **************************************************
+# 75% 238.94 11 ***************************************
+# 80% 240.45 11 ***************************************
+# 85% 241.96 10 ***********************************
+# 90% 243.47 8 ****************************
+# 95% 244.98 5 *****************
+# 100% 246.49 3 **********
+# over 0
+# approx. ln L -5542.7 ... -5589.1 diff 46.5, TBL 216.3 ... 228.5 diff 12.3
+((((Chimp,Bonobo),Human),Gorilla),Orang,Siamang); 0.0
+(((Chimp,Bonobo),Human),(Orang,Gorilla),Siamang); 17.2
+(((Chimp,Bonobo),(Human,Gorilla)),Orang,Siamang); 18.9
+((((Chimp,Bonobo),Gorilla),Human),Orang,Siamang); 19.1
+(((Chimp,Bonobo),Human),Orang,(Siamang,Gorilla)); 20.6
+((Chimp,Bonobo),((Orang,Gorilla),Human),Siamang); 41.2
+((Chimp,Bonobo),(Orang,Gorilla),(Siamang,Human)); 44.2
+((Chimp,Bonobo),(Orang,(Human,Gorilla)),Siamang); 46.2
+((Chimp,Bonobo),(Orang,Human),(Siamang,Gorilla)); 46.4
+((Chimp,Bonobo),((Orang,Human),Gorilla),Siamang); 46.5
Added: trunk/packages/molphy/trunk/debian/tests/compare/test6.tplq
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test6.tplq (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test6.tplq 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,2 @@
+1 / 3 A/B:4.00 F model approx ln L -5903.3 ... -5903.3 diff 0.0
+((((Chimp,Bonobo),Human),Gorilla),Orang,Siamang);
Added: trunk/packages/molphy/trunk/debian/tests/compare/test7.mlq
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test7.mlq (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test7.mlq 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,24 @@
+protml 2.3b3 (11/09/01) JTT-F 7 OTUs 409 sites. test7.ptn
+#1
+ :--1 Homo
+ :--8
+ : :----2 Drosophil
+:---10
+: : :---3 Saccharom
+: :---9
+: :----4 Mucor
+:
+: :-5 Arabidops
+:----11
+: :-6 Lycopersi
+:
+:-----------------------7 Sulpholob
+
+No.1 ext. branch S.E. int. branch S.E.
+Homo 1 5.69 1.32 8 2.54 1.00
+Drosophil 2 9.80 1.70 9 4.44 1.27
+Saccharom 3 8.31 1.60 10 6.06 1.71
+Mucor 4 9.17 1.65 11 10.81 2.04
+Arabidops 5 2.05 0.76 TBL : 126.70 iter: 6
+Lycopersi 6 1.18 0.60 ln L: -3155.25 +- 98.78
+Sulpholob 7 66.64 5.52 AIC : 6370.50
Added: trunk/packages/molphy/trunk/debian/tests/compare/test7.mls
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test7.mls (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test7.mls 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,52 @@
+protml 2.3b3 (11/09/01) JTT-F 7 OTUs 409 sites. test7.ptn
+#0
+:----1 Homo
+:
+:-----2 Drosophil
+:
+:-----3 Saccharom
+:
+:-----4 Mucor
+:
+:------5 Arabidops
+:
+:------6 Lycopersi
+:
+:-------------------------7 Sulpholob
+#1
+ :--1 Homo
+:-10
+: :----2 Drosophil
+:
+: :---3 Saccharom
+:---9
+: :----4 Mucor
+:
+: :-5 Arabidops
+:-------8
+: :-6 Lycopersi
+:
+:-------------------------7 Sulpholob
+
+ :--1 Homo
+ :-10
+ : :----2 Drosophil
+:---11
+: : :---3 Saccharom
+: :---9
+: :----4 Mucor
+:
+: :-5 Arabidops
+:-----8
+: :-6 Lycopersi
+:
+:-----------------------7 Sulpholob
+
+No.1 ext. branch S.E. int. branch S.E.
+Homo 1 5.69 1.32 8 10.81 2.04
+Drosophil 2 9.80 1.70 9 4.44 1.27
+Saccharom 3 8.31 1.60 10 2.54 1.00
+Mucor 4 9.17 1.65 11 6.06 1.71
+Arabidops 5 2.05 0.76 TBL : 126.70 iter: 6
+Lycopersi 6 1.18 0.60 ln L: -3155.25 +- 98.78
+Sulpholob 7 66.64 5.52 AIC : 6370.50
Added: trunk/packages/molphy/trunk/debian/tests/compare/test7.mls-2.2
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test7.mls-2.2 (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test7.mls-2.2 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,29 @@
+protml 2.2 Jul 2 1994 JTT-F 7 OTUs 409 sites test7.ptn
+
+(Homo,Drosophil,Saccharom,Mucor,(Arabidops,Lycopersi),Sulpholob);
+(Homo,Drosophil,(Saccharom,Mucor),(Arabidops,Lycopersi),Sulpholob);
+(Homo,Drosophil,(Saccharom,Mucor),((Arabidops,Lycopersi),Sulpholob));
+(Homo,Drosophil,((Saccharom,Mucor),((Arabidops,Lycopersi),Sulpholob)));
+
+:--1 Homo
+:
+:----2 Drosophil
+:
+: :---3 Saccharom
+: :---9
+: : :----4 Mucor
+:-11
+ : :-5 Arabidops
+ : :-----8
+ : : :-6 Lycopersi
+ :---10
+ :-----------------------7 Sulpholob
+
+No.1 num length S.E. num length S.E.
+Homo 1 5.65 1.31 8 10.74 2.03
+Drosophil 2 9.73 1.69 9 4.42 1.27
+Saccharom 3 8.26 1.59 10 6.03 1.70
+Mucor 4 9.11 1.64 11 2.53 0.99
+Arabidops 5 2.04 0.75 8
+Lycopersi 6 1.18 0.60 ln L: -3155.53 +- 98.80
+Sulpholob 7 66.34 5.49 AIC : 6371.06
Added: trunk/packages/molphy/trunk/debian/tests/compare/test7.tpl
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/compare/test7.tpl (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/compare/test7.tpl 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,2 @@
+1 / 3 JTT-F model approx ln L -3162.6 ... -3162.6 diff 0.0
+(((Homo,Drosophil),(Saccharom,Mucor)),(Arabidops,Lycopersi),Sulpholob);
Added: trunk/packages/molphy/trunk/debian/tests/comparetests
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/comparetests (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/comparetests 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,47 @@
+#!/bin/sh
+# This script is a helper script for testing the molphy components
+# It was written for the Debian GNU/Linux distribution by
+# Andreas Tille <tille at debian.org>
+
+echo Testing $1 ...
+COMPARE=/usr/share/doc/molphy/examples/tests/compare
+
+if [ _$1 = _ ] ; then
+ echo Usage: $0 "<test-result-to-compare>"
+ exit -1
+fi
+
+if [ ! -d $COMPARE ] ; then
+ echo Broken installation.
+ echo Directory $COMPARE with test results is missing.
+ exit -1
+fi
+
+if [ ! -f $1 ] ; then
+ echo $1 not found.
+ exit -1
+fi
+
+if [ ! -f ${COMPARE}/$1 -a ! -f ${COMPARE}/$1.gz ] ; then
+ echo Broken installation.
+ echo File ${COMPARE}/$1 with test results is missing.
+ exit -1
+fi
+
+## The first line contains the date the test was done so we have
+## to delete it for comparison ...
+
+if [ -f ${COMPARE}/$1 ] ; then
+ sed "1d" ${COMPARE}/$1 > $1.comp
+else
+ zcat ${COMPARE}/$1 | sed "1d" > $1.comp
+fi
+
+sed "1d" $1 > $1.test
+
+diff $1.comp $1.test
+
+if [ -f ${COMPARE}/$1-2.2 ] ; then
+ echo Note: There where explictite differences to molphy version 2.2
+ echo Please read ${COMPARE}/README.compare
+fi
Added: trunk/packages/molphy/trunk/debian/tests/makefile
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/makefile (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/makefile 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,70 @@
+#!/usr/bin/make
+
+# This makefile was written to test the output of the molphy components
+# It was written for the Debian GNU/Linux distribution by
+# Andreas Tille <tille at debian.org>
+
+all: comparetests protml nucml njdist
+ @echo All tests successfully done!
+
+protml: test4.ptn test5.ptn test15.ptn test15.cns
+ protml -e test4.ptn > test4.tpl
+ @comparetests test4.tpl
+ protml test4.ptn test4.tpl > test4.ml
+ @comparetests test4.ml
+ protml -e test5.ptn | tee test5.tpl | protml -b test5.ptn - > test5.ml
+ @comparetests test5.tpl
+ @comparetests test5.ml
+ protml -ef test15.ptn test15.cns > test15.tpl
+ @comparetests test15.tpl
+ protml -fb test15.ptn test15.tpl > test15.ml
+ @comparetests test15.ml
+ protml -sf test7.ptn > test7.mls
+ @comparetests test7.mls
+ protml -qf -n3 test7.ptn > test7.tpl
+ @comparetests test7.tpl
+ protml -fb test7.ptn test7.tpl > test7.mlq
+ @comparetests test7.mlq
+ @echo All $@ successfully done!
+
+nucml: test6.nuc
+ nucml -s test6.nuc > test6.mls
+ @comparetests test6.mls
+ nucml -q -n3 test6.nuc > test6.tplq
+ @comparetests test6.tplq
+ nucml -b -topt test6.nuc test6.tplq > test6.mlq
+ @comparetests test6.mlq
+ nucml -e -t30.58 -n10 test6.nuc > test6.tpl
+ @comparetests test6.tpl
+ nucml -b -t30.58 test6.nuc test6.tpl > test6.ml
+ @comparetests test6.ml
+ @echo All $@ successfully done!
+
+njdist: test4.ptn test15.tree
+ protml -D test4.ptn > test4.dis
+ @comparetests test4.dis
+ njdist test4.dis > test4.nj
+ @comparetests test4.nj
+ protml -D test5.ptn | njdist -w > test5.nj
+ @comparetests test5.nj
+ protml -D test15.ptn > test15.dis
+ @comparetests test15.dis
+ njdist test15.dis > test15.nj
+ @comparetests test15.nj
+ njdist -o 18 test15.dis > test15.njo
+ @comparetests test15.njo
+ njdist -o 18 -T test15.tree test15.dis > test15.njo
+ @comparetests test15.tree
+ @echo All $@ successfully done!
+
+clean:
+ rm -f *.comp *.test
+ rm -f protml.eps protml.tre
+ rm -f nucml.eps nucml.tre
+ rm -f njdist.eps njdist.tpl
+
+proper:
+ make clean
+ rm -f test4.tpl test4.ml test5.tpl test5.ml test15.tpl test15.ml test7.mls test7.tpl test7.mlq
+ rm -f test6.mls test6.tplq test6.mlq test6.tpl test6.ml
+ rm -f test4.dis test4.nj test5.nj test15.dis test15.nj test15.njo test15.tree.tre
Added: trunk/packages/molphy/trunk/debian/tests/test15.cns
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test15.cns (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test15.cns 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,9 @@
+(
+ {
+ ( (Homo,Xenopus), (Drosophil,Artemia) ),
+ ( (Saccharom,Candida), (Mucor,Absidia) ),
+ (Arabidops,Lycopersi)
+ },
+ Sulpholob,
+ (Thermococ,(Thermopla,(Methanoco,Halobacte)))
+);
Added: trunk/packages/molphy/trunk/debian/tests/test15.ptn
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test15.ptn (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test15.ptn 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,121 @@
+15 409 test15.ptn
+Homo
+EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAE
+RERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT
+REHALLAYTLGVKQLIVGVNKMDSYSQKRYEEIVKEVSTYIKKIGYDTVAFVPISGWNGD
+NMLEPSANMPWFKGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+LKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKN
+PPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPK
+FLKSGDAAIVDMVPGKPMCVESFSDYPPLGFAVRDMRQTVAVGVIKAVD
+Xenopus
+EKHIKIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAE
+RERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT
+REHALLAYTLGVKQLIVGINKMDSYSQKRYEEIVKEVSTYIKKIGYDTVAFVPISGWNGD
+NMLEPSPNMPWFKGTTLLEALDCILPPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+IKPGMVVTFAPVNVTTEVKSVEMHHEALTEAVPGDNVGFNVKNVSVKDVRRGNVAGDSKI
+PPMEAGSFTAQVIILNHPGQIGAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDNPK
+FLKSGDAAIVDMIPGKPMCVESFSDYPPLGFAVRDMRQTVALGVIKAVE
+Drosophil
+EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVQIDAAGTGISDQT
+REHALLAFTLGVKQLIVGVNKMDSYSEARYEEIKKEVSSYIKKVGYAAVAFVPISGWHGD
+NMLEPSTNMPWFKGKTLVDALDAILPPARPTDKALRLPLQDVYKIGGIGTVPVGRVETGV
+LKPGTVVVFAPANITTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDSKA
+PPKGAADFTAQVIVLNHPGQIANGYTPVLDCHTAHIACKFAEILEKVDRRSGKTTEENPK
+FIKSGDAAIVNLVPSKPLCVEAFQEFPPLGFAVRDMRQTVAVGVIKAVN
+Artemia
+EKHINIVVIGHVDSGKSTTTGHLIYKCGSIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT
+REHALLAYTLGVKQLIVGVNKMDSFSEARFEEIKKEVSAYIKKIDYAAVAFVPISGWHGD
+NMLEASDRLPWYKGKTLLDALDAILPPSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGI
+IKPGMIVTFAPANITTEVKSVEMHHESLEQASPGDNVGFNVKNVSVKELRRGYVASDSKN
+PARGSQDFFAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEAEPK
+FIKSGDAAMITLVPSKPLCVEAFSDFPPLGFAVRDMRQTVAVGVIKSVN
+Saccharom
+EKHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGISGQT
+REHALLAFTLGVRQLIVAVNKMDSWDESRFQEIVKETSNFIKKVGYKTVPFVPISGWNGD
+NMIEATTNAPWYKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+IKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKN
+PPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPK
+FLKSGDAALVKFVPSKPMCVEAFSEYPPLGFAVRDMRQTVAVGVIKSVD
+Candida
+EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETPKYHVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGISGQT
+REHALLAYTLGVKQLIVAVNKMDSWDKNRFEEIIKETSNFVKKVGYKTVPFVPISGWNGD
+NMIEPSTNCPWYKGKTLLEAIDAIEPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGI
+IKAGMVVTFAPAGVTTEVKSVEMHHEQLAEGVPGDNVGFNVKNVSVKEIRRGNVCGDSKN
+PPKGCDSFNAQVIVLNHPGQISAGYSPVLDCHTAHIACKFDTLVEKIDRRTGKKLEENPK
+FVKSGDAAIVKMVPTKPMCVEAFTDYPPLGFAVRDMRQTVAVGVIKSVE
+Mucor
+EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEEFKEAAELGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETPKYNVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGISGQT
+REHALLAFTLGFRQLIVAINKMDTWSQDRYNEIVKEVSGFIKKIGFKSVPFVPISGWHGD
+NMLDESTNMPWFKGKTLLEAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGT
+IKAGMVVNFAPAAVTTEVKSVEMHHETLTEGLPGDNVGFNVKNVSVKDIRRGNVCSDSKN
+PAKESASFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFSELIEKIDRRSGKKMEDSPK
+FVKSGDSAIVKMVPSKPMCVEAYTDYPPLGFAVRDMRQTVAVGVIKAVE
+Absidia
+EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETPKYHVTVIDAPGHRDFIKNMITGTSQADCGILIIAAGTGISGQT
+REHALLAFTLGVRQLIVAINKMDSWSEQRFNEIIKEVSGFIKKIGFKSVPFVPISGWHGD
+NMLEESTNMPWYKGKTLLDAIDAIDPPQRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+IKAGMVVTFAPANVTTEVKSVEMHHEQLVEGLPGDNVGFNVKNVSVKDIRRGNVCSDSKN
+PAKEAGSFTAQVIVLNHPGQIGAGYAPVLDCHTAHIACKFAELLEKIDRRSGKKLEDAPK
+FVKSGDSAIVKMIPSKPMCVEAYTDYPPLGFAVRDMRQTVAVGVIKAVE
+Arabidops
+EKHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE
+RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT
+REHALLAFTLGVKQMICCCNKMDAYSKARYDEIIKEVSSYLKKVGYDKIPFVPISGFEGD
+NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGM
+IKPGMVVTFAPTGLTTEVKSVEMHHESLLEALPGDNVGFNVKNVAVKDLKRGYVASNSKD
+PAKGAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKEIEKEPK
+FLKNGDAGMVKMTPTKPMVVETFSEYPPLGFAVRDMRQTVAVGVIKSVD
+Lycopersi
+EKHISIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE
+RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT
+REHALLAFTLGVKQMICCCNKMDAYSKARYDEIVKEVSSYLKKVGYDKIPFVPISGFEGD
+NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+IKPGMVVTFGPTGLTTEVKSVEMHHEALQEALPGDNVGFNVKNVAVKDLKRGYVASNSKD
+PAKGAASFTAQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKELEKEPK
+FLKNGDAGMVKMIPTKPMVVETFAEYPPLGFAVRDMRQTVAVGVVKNVD
+Sulpholob
+QKHLNLIVIGHVDHGKSTLIGRLLMDRGFIDEKTVKEAEAAKKLGKSEKYAFLMDRLKEE
+RERGVTINLSFMRFETRKYFFTVIDAPGHRDFVKNMITGASQADAAILVVSAKKGMSGQT
+REHIILSKTMGINQVIVAINKMDLYDEKRFKEIVDTVSKFMKSFGFNKVKFVPVVAPDGD
+NVTHKSTKMPWYNGPTLEELLDQLEIPPKPVDKPLRIPIQEVYSISGVGVVPVGRIESGV
+LKVGDKIVFMPVGKIGEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKDVKRGDVAGSVQN
+PPTVADEFTAQVIVIWHPTAVGVGYTPVLHVHTASIACRVSEITSRIDPKTGKEAEKNPQ
+FIKAGDSAIVKFKPIKELVAEKFREFPALGFAMRDMGKTVGVGVIIDVK
+Thermococ
+EKHINIVFIGHVDHGKSTTIGRLLFDTANIPENIIKKFEEMGEKGKSFKFAWVMDRLKEE
+RERGITIDVAHTKFETPHRYITIIDAPGHRDFVKNMITGASQADAAVLVVAVTDGVMPQT
+KEHAFLARTLGINNILVAVNKMDMYDEKKFKAVAEQVKKLLMMLGYKNFPIIPISAWEGD
+NVVKKSDKMPWYNGPTLIEALDQMPEPPKPTDKPLRIPIQDVYSIKGVGTVPVGRVETGV
+LRVGDVVIFEPASTIGEVKSIEMHHEPMQEALPGDNIGFNVRGVGKNDIKRGDVAGHTNN
+PPTVVRPFKAQIIVLNHPTAITVGYTPVLHAHTLQVAVRFEQLLAKLDPRTGNIVEENPQ
+FIKTGDSAIVVLRPTKPMVIEPVKEIPQMGFAIRDMGQTVAAGMVISIQ
+Thermopla
+QKHLNLITIGHVDHGKSTLVGRLLYEHGEIPAHIIEEYKEAEQKGKTFEFAWVMDRFKEE
+RERGVTIDLAHRKFETDKYYFTLIDAPGHRDFVKNMITGTSQADAAILVISARDGVMEQT
+REHAFLARTLGVPQMVVAINKMDAYSEKRYNEVKADAEKLLRSIGFKDISFVPISGYKGD
+NVTKPSPNMPWYKGPTLLQALDAFKVPEKPINKPLRIPVEDVYSITGIGTVPVGRVETGV
+LKPGDKVIFLPADKQGDVKSIEMHHEPLQQAEPGDNIGFNVRGIAKNDIKRGDVCGHLDT
+PPTVVKAFTAQIIVLNHPSVIAPGYKPVFHVHTAQVACRIDEIVKTLNPKDGTTLKEKPD
+FIKNGDVAIVKVIPDKPLVIEKVSEIPQLGFAVLDMGQTVAAGQCIDLE
+Methanoco
+TKILNVAFIGHVDAGKSTTVGRLLLDGGAIDPQLIVRLKEAEEKGKGFEFAYVMDGLKEE
+RERGVTIDVAHKKFPTAKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVNVDDGIQPQT
+REHVFLIRTLGVRQLAVAVNKMDTFSEADYNELKKMIDQLLKMIGFEQINFVPVASLHGD
+NVFKKSERNPWYKGPTIAEVIDGFQPPEKPTNLPLRLPIQDVYTITGVGTVPVGRVETGI
+IKPGDKVVFEPAGAIGEIKTVEMHHEQLPSAEPGDNIGFNVRGVGKKDIKRGDVLGHTTN
+PPTVATDFTAQIVVLQHPSVLTDGYTPVFHTHTAQIACTFAEIQKKLNPATGEVLEENPD
+FLKAGDAAIVKLIPTKPMVIESVKEIPQLGFAIRDMGMTVAAGMAIQVT
+Halobacte
+EQHQNLAIIGHVDHGKSTLVGRLLYETGSVPEHVIEQHEEAEEKGKGFEFAYVMDNLAEE
+RERGVTIDIAHQEFSTDTYDFTIVDCPGHRDFVKNMITGASQADNAVLVVAADDGVQPQT
+QEHVFLARTLGIGELIVAVNKMDLYGESEYKQVVEEVKDLLTQVRFENAKFIPVSAFEGD
+NIAEESEHTGWYDGEILLEALNELPAPEPPTDAPLRLPIQDVYTISGIGTVPVGRVETGI
+LNTGDNVSFQPSDVSGEVKTVEMHHEEVPKAEPGDNVGFNVRGVGKDDIRRGDVCGPADD
+PPSVAETFQAQIVVMQHPSVITEGYTPVFHAHTAQVACTVESIDKKIDPSSGEVAEENPD
+FIQNGDAAVVTVRPQKPLSIEPSSEIPELGFAIRDMGQTIAAGKVLGVN
Added: trunk/packages/molphy/trunk/debian/tests/test15.tree
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test15.tree (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test15.tree 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,5 @@
+(((((Homo:1.456,Xenopus:2.215):5.159,(Drosophil:5.257,Artemia:7.247):3.724)
+:1.075,((Saccharom:5.073,Candida:4.014):2.615,(Mucor:4.444,Absidia:2.810)
+:3.308):3.309):1.947,(Arabidops:1.604,Lycopersi:1.554):12.729):26.645,
+Sulpholob:33.726,(Thermococ:23.040,(Thermopla:23.538,(Methanoco:22.576,
+Halobacte:28.715):4.132):1.271):2.403);
Added: trunk/packages/molphy/trunk/debian/tests/test4.ptn
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test4.ptn (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test4.ptn 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,13 @@
+4 90 test4.ptn
+Data1
+MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMKPTLLTATSVFIIAFIHAPPVDK
+DGHREPVSGSGRVINTWADIINRANLGMEV
+Data2
+MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMKPTLLTATICFIIAFIHAPPVDK
+DGHREPVAGSGRVISTWADILNRANLGFEV
+Data3
+MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMKPTLLTATICFIVAFIHAPPVDK
+DGHREPVAGSGRVINTWADVLNRANLGMEV
+Data4
+MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMKPTLLAATACFVIAFIHAPPVDK
+DGHREPVAGSGRVIATWADVINRANLGMEV
Added: trunk/packages/molphy/trunk/debian/tests/test5.ptn
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test5.ptn (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test5.ptn 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,36 @@
+5 352 test5.ptn
+Tabac_chl
+MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDI
+DGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASVHEWLYNGGPYELIVLHFL
+LGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF
+NFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFG
+QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGF
+NFNQSVVDSQGRVINTWADIINRANLGMEVMHERNAHNFPLDLAAIEAPSTN
+Prochloro
+MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFIIAFIAAPPVDI
+DGIREPVAGSLMYGNNIISGAVVPSSNAIGLHFYPIWEAASMDEWLYNGGPYQLVVFHFL
+IGIFCYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPLGQGSFSDGMPLGISGTF
+NFMLVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETSENESQNYGYKFG
+QEEETYNIVAAHGYFGRLIFQYASFNNSRALHFFLAAWPVVGIWFTSLGISTMAFNLNGF
+NFNQSVMDSQGRVISTWADILNRANLGFEVMHERNAHNFPLDLAAVKAPSII
+Anacystis
+MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIVAFIAAPPVDI
+DGIREPVAGSLMYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVVFHFL
+IGVFCYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF
+NFMFVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQNYGYKFG
+QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTSLGISTMAFNLNGF
+NFNQSVLDSQGRVINTWADVLNRANLGMEVMHERNAHNFPLDLAAGEAPAIN
+Fremyella
+MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVIAFIAAPPVDI
+DGIREPVAGSLIYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFL
+LGCACYLGRQWELSYRLGMRPWICVAYSAPLASATAVFLIYPIGQGSFSDGMPLGISGTF
+NFMIVFQAEHNILLHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQNYGYKFG
+QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGVSTMAFNLNGF
+NFNQSVIDSQGRVIATWADVINRANLGMEVMHERNAHNFPLDLAAGEAPAIN
+Synechocy
+MTTTQLGLQEQSLWSRFCCWITSTSNRLYIGWFGVLMIPTLLTATTCFIIAFIAAPPVDI
+DGIREPIAGSLLYGNNIITAAVVPSSNAIALHFYPIWEAHSLDEWLYNGGPYQLNVFHFL
+IGIFCYLGRQWELSYRLGMRPWICVAYSAPVAAATATLLIYSIGQGSFSDGLPLGISGTF
+NFMLVLQAEHNVLMHPFHMLGVAGVFGGALFAAMHGSLVTSSLIRETTEVESQNQGYKFG
+QEEETYNIVAAHGYFGRLIFQYASFNNSRALHSFLGAWPVVGIWFAALAVCCFAFNLNGF
+NFNQSILDAQGRPVSTWADVINRANIGFEVMHERNVHNFPLDLASGDAPAIE
Added: trunk/packages/molphy/trunk/debian/tests/test6.nuc
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test6.nuc (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test6.nuc 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,145 @@
+6 1344 test6.nuc
+Chimp
+TAAATCATCCCGCACCAAACCAACCAAACGATCCACTACCCCCTACATTCACACCCCTCC
+TACGCTAGACACATCCAACAAATAATTCACACAAACCCCAACCCACTCAAATGCATCGAT
+CCCCCACCAAACACTTCTACAAAATAAAGAAAAAACCTCTATAATCACCCAACCACCCAA
+AAACTTATACACCAAGCACTCCCTACGCTAACCACAACACAACACAACCACCCACAAAAC
+AATCTCACTTTACTCCCATTCATGACCACCCCACAAATCCACGAAAATCATACCCCCAAC
+ACAATCCACAATCCAACAATTCCCCCCCACCCTCTCCTCCACACCCCATAATCATTCAAA
+AAACATAACCCCCTACCCTCAGTACCCCCAAACAGGCCCCAACTACCATTAAACAACTAA
+TACGCACATCTTGTAACAACCCATTCCCCTCCCACTACAACCCAAGTTACACTCCGATCG
+ATTCCCGACCCACCACCGCGCTTCATATATCAAACCGAATAACCTCAGACCGTTACCACA
+CCCCATGACCCTCAACTCCCAATTTAATTCGCACAACCCCACCACAACATCACCACATTC
+CCAAGATTCCCTCCCCACGAACTTATACACATTCCCATTTTCAACCAATCCTATTCCAAA
+AATATACGTATAAATCCAGTCGAACTATAAGACACCACTCCCTCACTTTTCCCAACCACT
+ATCACTGAATCAACACAGTCTCCCATCACCTAAACAAACCGACCACCCACCCCCTAAAAT
+ACCCAACCTCACCACACTCACACTCACATCCGCTCACACCCAGCCTCATGGCATCGCCCT
+ACCAATCAACACATCCGAAAAAATCGTAACTTAAAACAAAAGCCACGAAATACCACCCAC
+AACACAATAGATAGAATAATTTCTCAAATTCTCCTCCATCTCCCTACACCTCAACAAAAT
+TTTTACCGAAACCATCGCCCCACTTCAACGTCTCAACGCCCCCTTTAACCTAATACCACC
+CCCGACCCCCACCAATAAATTAACTCTTCAGCCATACCTTAATAAATTACAATTCAACAA
+ACATCACACACTCCCAAAAACCCACAACTAACCTTACCCAAACTAACTAAACACTAAGCA
+ATCCAACCATCCACGAATCCCAAAAATATCTACCAAACAAAACCTACAAAAAGCACCAAA
+CTACCTAGCCTTATCCCCAATCCAAAATAGCAAAAATACCTAAACATCAAACACTTTCAC
+TTTGTACCACAACCAATACACGTCCAAACAACACTCTGTATCACCCAGACATACTCCAAT
+CCATTCACTAAACACATACTCTTA
+Bonobo
+TAAATCATCCCACACCAAACCAACCAAACGATTCACTACCCCCTACATTCACACCCCTCC
+CACACTAGACACATCCAACAAATAATTCACACAAACCCCAATCCACTCAAACGCGTCAAT
+CCCCCACCAAACACCTCTACAAAATAATGAAAATACCTCCATAATCACCCAACCACCCAA
+AAACCCATACAACAAGCACTCCCTACGCTAACCACAACACAACACAACCACCCACAAAAT
+AACCTCACTTTATTTCCATTCACGACCACCCCACAAATCCACGAAAATTACACCCCCAAC
+ACAACCCGCAATCCAACAATTCCTCCCCACCCTCTCCTCCCCACCCCGCAATTACTTAAA
+AAATATAATCCCCTACCCTCAATACCCTCAAGCAGGCCCCAACTACCATTAAACAACCAA
+TATGCACATCTTATAACAACCTATCCCCTTCTCACTGCAACTCAAATCACACCCCGATCG
+ATTCCCGACCTACCACCACACTTCATATATCAAACCCAATGACCTCAAACTGTTACCACA
+CCCCGCGACCCTCAACTCCCAACTTAATTCACACAACTCCACCATAACATCACCACATTC
+CCAAAATTCCCTCCCCATGAACTTATACACATTCCCATCTTCAACCAATCCTATTCAAAA
+AACACACGTATAAATTCAGTTGAACTATAAAACACAACTCTCTCACTTTTCCCAACCGCT
+ATCACTGAATCAACACAGCCTCCCGTCACTTAAACAAACCAACCATCCACCCCCCAAAAT
+ACCCAACCTCACCATACTCACACTCACATCCACTCACACCCAACCTCGTAGCATCGCCTT
+ACCAATCAACACACCCAGAAAAATCATAACTTAAAACAAAAGCCACGGAGTACCACCCGC
+AACGCAATAGATAGAATAACCTCTCAAATTCTTCTCCATCTCCCCACGCCTCAACAAAAT
+TTTTACCGAAACCATCGCCCCACTTCTATATCTTAACGCCCCCTTTAACCTAATACCACC
+CCCAACCCCCACCAATAAACCAACTCTTCGGCCATACCTTAATAAATTACAATCCAACAA
+ACATCACACACTCCCAAAAACTCACAACTAACCTTACCCAGACCAACTAAACACTAAGCA
+ATCCAACCATCTACTAATTCCAAAAACATCTACCAAACAAAACCTACAAAAAGCACCAAG
+CTACCTAGTCCTATCCCCAATCCAAAATAGCAAAAATACCTAAACATCAAACATTTTCAT
+TTCATATCACAACCAATACACGTCCAAACAACACTCTGTATCACCCAGACATACTCCAAT
+CCATCCACTAAACACATACTCTTA
+Human
+TAAACCACCCCACACCAAACCAACCAAATAATCCACTACCCTCTACATTCGCACCCCTCC
+TACACCAGACGCATTCAACAAACGATTTATACAAACTTCAATCCGTCCGAACACACTAAT
+CCCCTACCAAACACTTCTACAAAACAATAAAAAAACCTCCACAGTCACCTGACCGTTCAA
+AAACCCACACACTCAACACTCCTCACACCAACTATAACGCGACACAACCATCCAAAAAAT
+AGCCTCACTTTATTTTCATTCACAACCACCCCGCAAATCCACGAAAAACATACCCCCAAC
+GCGACCTGCAGCTCAACAACTCCCCCCCACCCCCTCCCCCACACCCCACAACCATCCAAA
+AAGTATAACCACCCACCCTCGACATCCTTAAACAGGCCCTAACTACCACTAAACAACCAA
+TACACATACCTTACGGCGACCTATCCCCCCTCCACTATAACCCAAACCACACTCCAATCA
+ACTCCTGGTCCACCACCACATCTCACGCATTAGGCAAAATAACCTCAAGCCCCTACCACA
+CCCCACAATCCTCAGCCTCCAATCTAACTCACACAGCCCCACCACAACATCATCACATTC
+CTAAAACCCCCCCCCCCCAAACCTACACACATCTCTATTTTCAACCAACCTTATCCCAAA
+AATACATGCATGAATCCAGTCGAACTATAAAACACAAATCCCTCACCTCCCCCAATCACC
+ACCACTGAATTAGCACAACCTTCCATCGTCTAAACAAACCAACCGCCTACCCCTCAAAAT
+ATCCAACCTCATCACACCCACACCCACTCTCACCCATATCCAACTCCACAGCATCGCCCT
+ACCAACCAATACACTTAAAAAAATCGTAACCTGGAACAAAAACCACGGAATACCACCCAC
+AACACAATAGATAGAATAACTTCTCAAGTCCTTTCCCACTCTCCCACGTCTCAACAAAAT
+TTCCACTGAAACCATCGCCCCACCCCCACACCTCAACGCCTCCTCCAATCCAGCACCGCC
+CCCAACCCCCATCAACAAACCGACTCTCTAAACGTACCTTAATAAACCGCAATCCAACAA
+ATATCATACACTCCTAAGGACCTACTACTAACCTCGCCCAAATCAACTAAGCATCAAGCA
+ATTCAGCCATCCACTAACCCCAAAAACACCCATCAAGCAAAATTCACAAAAAGCACCAAG
+CTATCTAGCCCCATCCCCAACCCAAAACAACAAAGACACCTAAACATTAAACACTTTCAT
+CCCACGTCATAACCAATACACGCCCAAGCAGTACTCTGTATCACCCAAACATACTCCAAT
+TCACCCACTAAACGCACACTCTTA
+Gorilla
+TATATTATCCCACGCCGAACCGACCGAACAATTCATCACCCTCTACATCCGCACCCCTCC
+CACTTTAAACCCATTCAACAAACAATTCACACAAATCCCAACCCATCCAAATACACCAAC
+CCCCCACCAAACACTCTTACAAAGCAATATAAAAACCTCCAGAACCACCCAGTCACCCAA
+AAACTGACACATCGAATACTCCTTACACCAACCACAACATAACGTAACCACCTAAAAAAT
+AATCTTATTTTGCTTTCCTTCACAACCACCCCACAAATTTATAGAAAATACCCCCCCAAT
+ACAACCCACAGTTCAACAATCCCTCCCTGCCCCCCCCTCTACATCCCTCAAACACCCAGA
+AAGCATTACTCCCTATCACCCATACCCCCAAATAGGCCCCAACTACTATTAAATAACCAA
+TACACACATCTTAAATTAACCTATCTCCTTTCCACTGCAATCCAAGTCACACTCCGAACA
+ATTCCCGACCCACCACCACTCTTCATGCACTAAACCAGTTGACCTCAAATTCCCATTACA
+CTTCACAACCCTTAGCCCCTAACCTAACCCACACAACTCCACCACAACATTATCAAATTA
+TCAAAACTCCCCCTCCACAAATTCACACACATTACCATCTACAACCAACCCTATTCCAAA
+AACATATACATAAATTCGATTGACCCATAAAACATAACCCCCTCACCTCCCCCAACCACT
+ACTATTCAATCAGCACAGCTTCCTACCACCCAAACGAATCGGCCATCCATCCCTCATAAT
+GCCCAGCTTCATCACACCTATACCCACCTCCACTCTTACCCAACTTCATAACATCGCCCT
+ATTAATCGACGCACTCAAAAAAATTACAACCCAAAACAACAACCATGGAGTACTACTTAT
+AGTATAGTAGATAGAATAACTTTTCAAAACCTTTTCCACTTCCCCACGCCTCAACAAGAT
+CCCCACCAAAGCCACCGCTTCACGCCCATAACCTGATACTCCCCTCAACTCAACACCACC
+CTTAGCTCCTACCAACAAATCAACTCCCCAACTATACCCTAATACATCACAATTCAACAA
+ACACCGCGCACACCCAAAAACCCGCAACTACCCTTGCTTAGACCAACTAAACACCAAGCG
+ATCCAGCCATCAACCAATCTCAAATACATCCACCAAATAAAACCTACAAAAAGCACCAAA
+TCATCTAGCCCCATCCCCAGTCCAGAACAACAAAAATATCCGAACACTGAAAATTTTCAC
+CCCACGCCACAATCGATACGCACCCGAACAATACTCCGTATCACCAAAACCTACTCTAAC
+CTACCCACCAAACATACACTCCTA
+Orang
+TAAACCACCCCACGCCAAATCGACCAAAAAACCCACTACTCTCAACATCCATACCCCCCC
+CACATTAAGCCCACTCAGCAAACACTCCACACAAACCCCAACTCATCCAAACACATCAAC
+CCCCCATCAGACACTCCCATATAATACCAAAAAAACCCCCACAACCAACCAACCACCTAA
+AAACCTATACAACAAACACCCCCCATATCGACCACAACACAACACGACCACTCAAAAAAA
+ACCCACCTCCCACCTTCGATCACATCCACTCCACAGACCCACAGAAAACACAACAACAGC
+GCAACCCACAATCTGACAACCTTTTCACACTCTCCCCCCCACATCCCACAACCGTCCAAA
+AAACATAACCTCCCACTCTCCATATCCTCCACCAAGCCCCGACCGCCATTAGACGGCCAA
+TTCACTCACCCTTTAACACCCCATTCTTCTCCCACTACAATTCGCGCAATACTCCAAGCG
+ATCCTTGACGCATCACCACCCCCCCAACTTTAAGCAAAGCAACTACAAACCTCAACTACG
+ACCTACAACTCATAGTCTCTAATTTAACTAACATATCCCCAACGCAACATCCCCACACTC
+CCAAAACCCATTACTCGTATGTTCACACACATCCCTACCTCCAATCCACCCCAACCCAAA
+AATGTACACACACATTCGTTCAACCCACAAGACGCAACCCCCTCATTCCCCCCAATCACT
+ACCACCTAATCACCACAACTCCCCACCAACCAGACAAACCAACTACCTACCTCCCAAAAT
+ACCCAACCCCGCAACACCCACGCTTATCCCCATCCATACCCGATCTCAATACACCCTCCC
+ATCAATTAACACATCCAAATAAATCATAACTCAAAACAATAATCACAGGACACCACCTGT
+AACCTAACAGGCAAGATAACTCTTCAAAGCCTCCCCCACCCACCCACGCCTCAACAGACC
+CTCCATCAGAATTATCAACCCATACCCATACCCCAACACCCTCCCTAACCTAGCACCGTT
+CTCAGCCCTCGCAAACAAACCTACACCCTAACCACACCTCAACACACCGCAACCCAACGA
+ACACCACACACACTCAAAAATTCACAACTATCCCTGTCCAAACCAACCAAACACTAAGCA
+ATCCAGCCCCTAATTAACCCCGAAAACACCCACCAAATCAAACCCACAAAAAGCCCTATA
+CCATCCAACTCCATCCCCTATCCGAAACACCAAAAACCTCTAAATACAAAACACTTCCAC
+CCCACCCCATAATCGACACATAACCAAACGACGCACCGCATCATCCGAATCCACCCCAAT
+TTACTTTTTAGACACACACCCCTA
+Siamang
+CAAATCACCCTACACCAAGCCGACCGCACAACTTACTATCTTTCACATCCATACCCCACT
+TATACTCATCACACCCAACAAACGACTCACAAAAACTCCAACTTGTCCAAACACACTAAC
+CCTTCATCAAACACCTCCACAAAACAACACAAAAACCCCCACAACTAATCCACCAACCAA
+AAACTCATACACCAAACACCCCATATATCAACCACAACACAACATGACCACCTACAAACA
+TACCACCCTCCATCCCAAACTACAACCATCCCACAAACCCACAACAAACACACCAAAAAG
+ATAACCCACAGTCTAGCAACTTCTCATTACCCCTCCACCCACACCCCACAACTACCTAAA
+AAATACAACATCCCACTCCCTTCAACCACACTCAAGCCCCGACCACTATTAAACGATCAA
+CACACACACCTCACAATACCTCGCTCCTTCCCAACCGCCACTCAAACTGTGCTCCAACTA
+ACACCCGACTTATCACCGTTTCTCAAGTCCCAAACCCAAAAACTCAGAACTCCAACTTTA
+CTTTACGTAAATCAGTTCCTTACCCAACATACATAATCTCACCATAACACTCCAATACTC
+CCAAAACTCCCCTCTCATAAACCTATACACGTTCCCATCTTCAACCAATACCATCCGAAG
+GACATACACACAAATCCATCTCACCTATAACGCACAACTTACCCATTCTCTTCAATCGCC
+ACCATCCAACTAACACACCTCCTAAGCATTCAAATAAGCTATCCACTCACTCCTCACAAC
+ACTCAACCCCACCACGCCTATACTCATCCCTATAAACACCTAACCCCGCAATATTCCCTT
+ACTCACCACTGCATCTAAAAAAATCACAGTCCAGAACAACAGCCTCAGGGCACAATTCAT
+AGCCTAATAGATATAACAACTACTCAAAACTCCCTCCACTCTCCCACATCCCAACAAAAC
+CTTTGCCAGAACCAACATTTTATATCCACCCCTCAACACCCCCTTCGACTTGACACCATA
+CCTGACCTTCAAAAATAAGGCTACTACCCAATTATACTCTAATAAACCACAATCCCATTA
+GTTCCACACACACCCACAAACCCACAACTGCCTCTAGTTAAATCAACCGAGTATCAAGCA
+ACCCGATACCAAATCAACCCAAAAAACGCCTACCCAACACTACCCCCAACAAGCACCAAA
+TTATCCAATTTCACCCCTAATCCAAAATAGCAAAAAAACCTAAACACCAATTATTCTTAT
+CCTCCACCACAACCGACACACAATCAAACTGCATATCACACTTTCTACACATGCCTCAAT
+CCATCTATCACGCACAAATATTAA
Added: trunk/packages/molphy/trunk/debian/tests/test7.ptn
===================================================================
--- trunk/packages/molphy/trunk/debian/tests/test7.ptn (rev 0)
+++ trunk/packages/molphy/trunk/debian/tests/test7.ptn 2008-03-03 07:16:47 UTC (rev 1498)
@@ -0,0 +1,57 @@
+7 409 test7.ptn
+Homo
+EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAE
+RERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT
+REHALLAYTLGVKQLIVGVNKMDSYSQKRYEEIVKEVSTYIKKIGYDTVAFVPISGWNGD
+NMLEPSANMPWFKGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+LKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKN
+PPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPK
+FLKSGDAAIVDMVPGKPMCVESFSDYPPLGFAVRDMRQTVAVGVIKAVD
+Drosophil
+EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVQIDAAGTGISDQT
+REHALLAFTLGVKQLIVGVNKMDSYSEARYEEIKKEVSSYIKKVGYAAVAFVPISGWHGD
+NMLEPSTNMPWFKGKTLVDALDAILPPARPTDKALRLPLQDVYKIGGIGTVPVGRVETGV
+LKPGTVVVFAPANITTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDSKA
+PPKGAADFTAQVIVLNHPGQIANGYTPVLDCHTAHIACKFAEILEKVDRRSGKTTEENPK
+FIKSGDAAIVNLVPSKPLCVEAFQEFPPLGFAVRDMRQTVAVGVIKAVN
+Saccharom
+EKHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGISGQT
+REHALLAFTLGVRQLIVAVNKMDSWDESRFQEIVKETSNFIKKVGYKTVPFVPISGWNGD
+NMIEATTNAPWYKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+IKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKN
+PPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPK
+FLKSGDAALVKFVPSKPMCVEAFSEYPPLGFAVRDMRQTVAVGVIKSVD
+Mucor
+EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEEFKEAAELGKSFKYAWVLDKLKAE
+RERGITIDIALWKFETPKYNVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGISGQT
+REHALLAFTLGFRQLIVAINKMDTWSQDRYNEIVKEVSGFIKKIGFKSVPFVPISGWHGD
+NMLDESTNMPWFKGKTLLEAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGT
+IKAGMVVNFAPAAVTTEVKSVEMHHETLTEGLPGDNVGFNVKNVSVKDIRRGNVCSDSKN
+PAKESASFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFSELIEKIDRRSGKKMEDSPK
+FVKSGDSAIVKMVPSKPMCVEAYTDYPPLGFAVRDMRQTVAVGVIKAVE
+Arabidops
+EKHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE
+RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT
+REHALLAFTLGVKQMICCCNKMDAYSKARYDEIIKEVSSYLKKVGYDKIPFVPISGFEGD
+NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGM
+IKPGMVVTFAPTGLTTEVKSVEMHHESLLEALPGDNVGFNVKNVAVKDLKRGYVASNSKD
+PAKGAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKEIEKEPK
+FLKNGDAGMVKMTPTKPMVVETFSEYPPLGFAVRDMRQTVAVGVIKSVD
+Lycopersi
+EKHISIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE
+RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT
+REHALLAFTLGVKQMICCCNKMDAYSKARYDEIVKEVSSYLKKVGYDKIPFVPISGFEGD
+NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGV
+IKPGMVVTFGPTGLTTEVKSVEMHHEALQEALPGDNVGFNVKNVAVKDLKRGYVASNSKD
+PAKGAASFTAQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKELEKEPK
+FLKNGDAGMVKMIPTKPMVVETFAEYPPLGFAVRDMRQTVAVGVVKNVD
+Sulpholob
+QKHLNLIVIGHVDHGKSTLIGRLLMDRGFIDEKTVKEAEAAKKLGKSEKYAFLMDRLKEE
+RERGVTINLSFMRFETRKYFFTVIDAPGHRDFVKNMITGASQADAAILVVSAKKGMSGQT
+REHIILSKTMGINQVIVAINKMDLYDEKRFKEIVDTVSKFMKSFGFNKVKFVPVVAPDGD
+NVTHKSTKMPWYNGPTLEELLDQLEIPPKPVDKPLRIPIQEVYSISGVGVVPVGRIESGV
+LKVGDKIVFMPVGKIGEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKDVKRGDVAGSVQN
+PPTVADEFTAQVIVIWHPTAVGVGYTPVLHVHTASIACRVSEITSRIDPKTGKEAEKNPQ
+FIKAGDSAIVKFKPIKELVAEKFREFPALGFAMRDMGKTVGVGVIIDVK
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