[med-svn] r5979 - trunk/packages/phyml/trunk/debian

[Andreas Tille]

Author: tille
Date: 2011-02-14 16:23:16 +0000 (Mon, 14 Feb 2011)
New Revision: 5979

Added:
   trunk/packages/phyml/trunk/debian/manpages
   trunk/packages/phyml/trunk/debian/phyml.1
Modified:
   trunk/packages/phyml/trunk/debian/changelog
Log:
Uploaded new upstream including newly written manpage


Modified: trunk/packages/phyml/trunk/debian/changelog
===================================================================
--- trunk/packages/phyml/trunk/debian/changelog	2011-02-14 15:43:16 UTC (rev 5978)
+++ trunk/packages/phyml/trunk/debian/changelog	2011-02-14 16:23:16 UTC (rev 5979)
@@ -1,9 +1,10 @@
-phyml (2:20100720-1) UNRELEASED; urgency=low
+phyml (2:20100720-1) unstable; urgency=low
 
   * New upstream version
   * Fixed watch file
   * Standard-Version: 3.9.1 (no changes needed)
   * Source format 3.0 (quilt)
+  * Wrote man page
 
  -- Andreas Tille <tille at debian.org>  Mon, 14 Feb 2011 15:04:52 +0100
 

Added: trunk/packages/phyml/trunk/debian/manpages
===================================================================
--- trunk/packages/phyml/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/phyml/trunk/debian/manpages	2011-02-14 16:23:16 UTC (rev 5979)
@@ -0,0 +1 @@
+debian/*.1

Added: trunk/packages/phyml/trunk/debian/phyml.1
===================================================================
--- trunk/packages/phyml/trunk/debian/phyml.1	                        (rev 0)
+++ trunk/packages/phyml/trunk/debian/phyml.1	2011-02-14 16:23:16 UTC (rev 5979)
@@ -0,0 +1,247 @@
+.TH PhyML "1" "3.0" "phyml " "User Commands"
+.SH NAME
+phyml \- Phylogenetic estimation using Maximum Likelihood
+.SH SYNOPSIS:
+.PP
+phyml [command args]
+
+.IP
+All the options below are optional (except '\-i' if you want to use the command\-line interface).
+.PP
+
+Command options:
+
+.HP
+\fB-i\fR (or \fB\-\-input\fR) \fIseq_file_name\fR
+.IP
+\fIseq_file_name\fR is the name of the nucleotide or amino\-acid sequence file in PHYLIP format.
+.PP
+
+.HP
+\fB\-d\fR (or \fB\-\-datatype\fR) \fIdata_type\fR
+.IP
+\fIdata_type\fR is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic',
+(use NEXUS file format and the 'symbols' parameter here).
+.PP
+
+.HP
+\fB\-q\fR (or \fB\-\-sequential\fR)
+.IP
+Changes interleaved format (default) to sequential format.
+.PP
+
+.HP
+\fB\-n\fR (or \fB\-\-multiple\fR) \fInb_data_sets\fR
+.IP
+\fInb_data_sets\fR is an integer corresponding to the number of data sets to analyse.
+.PP
+
+.HP
+\fB\-p\fR (or \fB\-\-pars\fR)
+.OP
+Use a minimum parsimony starting tree. This option is taken into account when the '\-u' option
+is absent and when tree topoLOGy modifications are to be done.
+
+.HP
+\fB\-b\fR (or \fB\-\-bootstrap\fR) \fIint\fR
+.IP
+\fIint > 0:\fR int is the number of bootstrap replicates.
+.IP
+\fIint = 0:\fR neither approximate likelihood ratio test nor bootstrap values are computed.
+.IP
+\fIint = \-1\fR: approximate likelihood ratio test returning aLRT statistics.
+.IP
+\fIint = \-2\fR: approximate likelihood ratio test returning Chi2\-based parametric branch supports.
+.IP
+\fIint = \-4\fR: (default) SH\-like branch supports alone.
+
+.HP
+\fB\-m\fR (or \fB\-\-model\fR) \fImodel\fR
+.IP
+model : substitution model name.
+\- \fINucleotide\fR\-based models : \fIHKY85\fR (default) | \fIJC69\fR | \fIK80\fR | \fIF81\fR | \fIF84\fR | \fITN93\fR | \fIGTR\fR | \fIcustom\fR
+(for the custom option, a string of six digits identifies the model. For instance, 000000)
+.IP
+corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
+012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.
+.IP
+\- \fIAmino\-acid\fR based models : \fILG\fR (default) | \fIWAG\fR | \fIJTT\fR | \fIMtREV\fR | \fIDayhoff\fR | \fIDCMut\fR | \fIRtREV\fR | \fICpREV\fR | \fIVT\fR
+\fIBlosum62\fR | \fIMtMam\fR | \fIMtArt\fR | \fIHIVw\fR |
+\fIHIVb\fR | \fIcustom\fR
+
+.HP
+\fB\-\-aa_rate_file\fR \fIfilename\fR
+.IP
+\fIfilename\fR is the name of the file that provides the amino acid substitution rate matrix in PAML format.
+It is compulsory to use this option when analysing amino acid sequences with the `custom' model.
+.PP
+
+.HP
+\fB\-f\fR \fIe\fR, \fIm\fR, or \fIfA,fC,fG,fT\fR
+.IP
+\fIe\fR : the character frequencies are determined as follows :
+.IP
+\- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting
+the occurence of the different bases in the alignment.
+.IP
+\- Amino\-acid sequences: (Empirical) the equilibrium amino\-acid frequencies are estimated by counting
+the occurence of the different amino\-acids in the alignment.
+.IP
+\fIm\fR : the character frequencies are determined as follows :
+.IP
+\- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood
+.IP
+\- Amino\-acid sequences: (Model) the equilibrium amino\-acid frequencies are estimated using
+the frequencies defined by the substitution model.
+.IP
+\fI"fA,fC,fG,fT"\fR : only valid for nucleotide\-based models. fA, fC, fG and fT are floating numbers that
+correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between
+your values of nucleotide frequencies, only commas!)
+
+.HP
+\fB\-t\fR (or \fB\-\-ts\fR/tv) \fIts/tv_ratio\fR
+.IP
+\fIts/tv_ratio\fR : transition/transversion ratio. DNA sequences only.
+Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.
+
+.HP
+\fB\-v\fR (or \fB\-\-pinv\fR) \fIprop_invar\fR
+.IP
+\fIprop_invar\fR: proportion of invariable sites.
+Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.
+
+.HP
+\fB\-c\fR (or \fB\-\-nclasses\fR) \fInb_subst_cat\fR
+.IP
+\fInb_subst_cat\fR : number of relative substitution rate categories. Default: \fInb_subst_cat=4\fR.
+Must be a positive integer.
+
+.HP
+\fB\-a\fR (or \fB\-\-alpha\fR) \fIgamma\fR
+.IP
+\fIgamma\fR : distribution of the gamma distribution shape parameter.
+Can be a fixed positive value or \fIe\fR to get the maximum likelihood estimate.
+
+.HP
+\fB\-s\fR (or \fB\-\-search\fR) \fImove\fR
+.IP
+Tree topoLOGy search operation option.
+Can be either \fINNI\fR (default, fast) or \fISPR\fR (a bit slower than NNI) or \fIBEST\fR (best of NNI and SPR search).
+
+.HP
+\fB\-u\fR (or \fB\-\-inputtree\fR) \fIuser_tree_file\fR
+.IP
+\fIuser_tree_file\fR : starting tree filename. The tree must be in Newick format.
+
+.HP
+\fB\-o\fR \fIparams\fR
+.IP
+This option focuses on specific parameter optimisation.
+.IP
+\fIparams\fR=tlr : tree topoLOGy (t), branch length (l) and rate parameters (r) are optimised.
+.IP
+\fIparams\fR=tl  : tree topoLOGy and branch length are optimised.
+.IP
+\fIparams\fR=lr  : branch length and rate parameters are optimised.
+.IP
+\fIparams\fR=l   : branch length are optimised.
+.IP
+\fIparams\fR=r   : rate parameters are optimised.
+.IP
+\fIparams\fR=n   : no parameter is optimised.
+
+.HP
+\fB\-\-rand_start\fR
+.IP
+This option sets the initial tree to random. It is only valid if SPR searches are to be performed.
+
+.HP
+\fB\-\-n_rand_starts\fR \fInum\fR
+.IP
+\fInum\fR is the number of initial random trees to be used.
+It is only valid if SPR searches are to be performed.
+
+.HP
+\fB\-\-r_seed\fR \fInum\fR
+.IP
+\fInum\fR is the seed used to initiate the random number generator.
+Must be an integer.
+
+.HP
+\fB\-\-print_site_lnl\fR
+.IP
+Print the likelihood for each site in file *_phyml_lk.txt.
+.PP
+
+.HP
+\fB\-\-print_trace\fR
+.IP
+Print each phyLOGeny explored during the tree search process
+in file *_phyml_trace.txt.
+
+.HP
+\fB\-\-run_id\fR \fIID_string\fR
+.IP
+Append the string \fIID_string\fR at the end of each PhyML output file.
+This option may be useful when running simulations involving PhyML.
+.PP
+
+.HP
+\fB\-\-quiet\fR
+.IP
+No interactive question (for running in batch mode) and quiet output.
+.PP
+
+.HP
+\fB\-\-no_memory_check\fR
+.IP
+No interactive question for memory usage (for running in batch mode). Normal ouput otherwise.
+.PP
+
+.HP
+\fB\-\-alias_subpatt\fR
+.IP
+Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations.
+See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example.
+.PP
+
+.HP
+\fB\-\-boot_progress_display\fR \fInum\fR (default=20)
+.IP
+\fInum\fR is the frequency at which the bootstrap progress bar will be updated.
+Must be an integer.
+
+.SH PHYLIP\-LIKE INTERFACE
+.PP
+You can also use PhyML with no argument, in this case change the value of
+a parameter by typing its corresponding character as shown on screen.
+
+.SH EXAMPLES
+.PP
+DNA interleaved sequence file, default parameters :
+.IP
+\fBphyml \-i seqs1\fR
+.PP
+AA interleaved sequence file, default parameters :
+.IP
+\fBphyml \-i seqs2 \-d aa\fR
+.TP
+AA sequential sequence file, with customization :
+.IP
+\fBphyml \-i seqs3 \-q \-d aa \-m JTT \-c 4 \-a e\fR
+
+.SH "SEE ALSO"
+.PP
+A simple, fast, and accurate algorithm to estimate large phyLOGenies by maximum likelihood
+.PP
+Stephane Guindon and Olivier Gascuel,
+Systematic BioLOGy 52(5):696\-704, 2003.
+.PP
+Please cite this paper if you use this software in your publications.
+
+.SH AUTHOR
+\fBPhyML\fP was written by Stephane Guindon and Olivier Gascuel
+and others
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian project (but may be used by others).