[med-svn] r11357 - in trunk/packages/fasttree/trunk/debian: . patches
Thorsten Alteholz
alteholz at alioth.debian.org
Fri Jun 15 18:05:05 UTC 2012
Author: alteholz
Date: 2012-06-15 18:05:04 +0000 (Fri, 15 Jun 2012)
New Revision: 11357
Added:
trunk/packages/fasttree/trunk/debian/fasttree.1
trunk/packages/fasttree/trunk/debian/fasttree.upstream-metadata.yaml
trunk/packages/fasttree/trunk/debian/fasttreeMP.1
trunk/packages/fasttree/trunk/debian/get-orig-source
trunk/packages/fasttree/trunk/debian/manpages
trunk/packages/fasttree/trunk/debian/watch
Removed:
trunk/packages/fasttree/trunk/debian/README.Debian
Modified:
trunk/packages/fasttree/trunk/debian/changelog
trunk/packages/fasttree/trunk/debian/compat
trunk/packages/fasttree/trunk/debian/control
trunk/packages/fasttree/trunk/debian/copyright
trunk/packages/fasttree/trunk/debian/fasttree.install
trunk/packages/fasttree/trunk/debian/patches/Makefile.patch
trunk/packages/fasttree/trunk/debian/rules
Log:
fasttree finalized
Deleted: trunk/packages/fasttree/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fasttree/trunk/debian/README.Debian 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/README.Debian 2012-06-15 18:05:04 UTC (rev 11357)
@@ -1,9 +0,0 @@
-fasttree for Debian
--------------------
-
-Please help with
-
- * man pages
- * get-orig-source - upstream is only a file
-
- -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 18:52:56 +0100
Modified: trunk/packages/fasttree/trunk/debian/changelog
===================================================================
--- trunk/packages/fasttree/trunk/debian/changelog 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/changelog 2012-06-15 18:05:04 UTC (rev 11357)
@@ -1,5 +1,5 @@
-fasttree (2.1.0.c-1) UNRELEASED; urgency=low
+fasttree (2.1.4-1) unstable; urgency=low
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #677648)
- -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 18:52:56 +0100
+ -- Thorsten Alteholz <debian at alteholz.de> Fri, 15 Jun 2012 19:52:56 +0200
Modified: trunk/packages/fasttree/trunk/debian/compat
===================================================================
--- trunk/packages/fasttree/trunk/debian/compat 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/compat 2012-06-15 18:05:04 UTC (rev 11357)
@@ -1 +1 @@
-7
+9
Modified: trunk/packages/fasttree/trunk/debian/control
===================================================================
--- trunk/packages/fasttree/trunk/debian/control 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/control 2012-06-15 18:05:04 UTC (rev 11357)
@@ -3,9 +3,10 @@
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 7.0.50~)
-Standards-Version: 3.9.1
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
Homepage: http://www.microbesonline.org/fasttree/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fasttree/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk/
@@ -28,5 +29,8 @@
for the varying rates of evolution across sites, FastTree uses a single
rate for each site (the "CAT" approximation). To quickly estimate the
reliability of each split in the tree, FastTree computes local support
- values with the Shimodaira-Hasegawa test (these are the same as PhyML
- 3's "SH-like local supports").
+ values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's
+ "SH-like local supports").
+ .
+ This package contains a single threaded version (fasttree) and a
+ parallel version which uses OpenMP (fasttreMP).
Modified: trunk/packages/fasttree/trunk/debian/copyright
===================================================================
--- trunk/packages/fasttree/trunk/debian/copyright 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/copyright 2012-06-15 18:05:04 UTC (rev 11357)
@@ -8,6 +8,7 @@
Files: debian/*
Copyright: 2011 Steffen Moeller <moeller at debian.org>
+ 2012 Thorsten Alteholz <debian at alteholz.de>
License: GPL-2.0+
License: GPL-2.0+
Added: trunk/packages/fasttree/trunk/debian/fasttree.1
===================================================================
--- trunk/packages/fasttree/trunk/debian/fasttree.1 (rev 0)
+++ trunk/packages/fasttree/trunk/debian/fasttree.1 2012-06-15 18:05:04 UTC (rev 11357)
@@ -0,0 +1,339 @@
+.TH "fasttree" "1" "June 2012" "Lawrence Berkeley National Lab" "User Commands"
+.SH NAME
+fasttree \- create phylogenetic trees from alignments of nucleotide or protein sequences
+.SH DESCRIPTION
+fasttree infers approximately-maximum-likelihood phylogenetic trees from
+alignments of nucleotide or protein sequences. It handles alignments
+with up to a million of sequences in a reasonable amount of time and memory.
+
+fasttree is more accurate than PhyML 3 with default settings, and much
+more accurate than the distance-matrix methods that are traditionally
+used for large alignments. fasttree uses the Jukes-Cantor or generalized
+time-reversible (GTR) models of nucleotide evolution and the JTT
+(Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
+for the varying rates of evolution across sites, fasttree uses a single
+rate for each site (the "CAT" approximation). To quickly estimate the
+reliability of each split in the tree, fasttree computes local support
+values with the Shimodaira-Hasegawa test (these are the same as PhyML
+3's "SH-like local supports").
+.SH SYNOPSIS
+.PP
+.B fasttree protein_alignment > tree
+.PP
+.B fasttree \fB\-nt\fR nucleotide_alignment > tree
+.PP
+.B fasttree \fB\-nt\fR \fB\-gtr\fR < nucleotide_alignment > tree
+.PP
+fasttree accepts alignments in fasta or phylip interleaved formats
+.SS "Common options (must be before the alignment file):"
+.HP
+\fB\-quiet\fR to suppress reporting information
+.HP
+\fB\-nopr\fR to suppress progress indicator
+.HP
+\fB\-log\fR logfile \fB\-\-\fR save intermediate trees, settings, and model details
+.HP
+\fB\-fastest\fR \fB\-\-\fR speed up the neighbor joining phase & reduce memory usage
+.IP
+(recommended for >50,000 sequences)
+.HP
+\fB\-n\fR <number> to analyze multiple alignments (phylip format only)
+.IP
+(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
+.HP
+\fB\-nosupport\fR to not compute support values
+.HP
+\fB\-intree\fR newick_file to set the starting tree(s)
+.HP
+\fB\-intree1\fR newick_file to use this starting tree for all the alignments
+.IP
+(for faster global bootstrap on huge alignments)
+.HP
+\fB\-pseudo\fR to use pseudocounts (recommended for highly gapped sequences)
+.HP
+\fB\-gtr\fR \fB\-\-\fR generalized time\-reversible model (nucleotide alignments only)
+.HP
+\fB\-wag\fR \fB\-\-\fR Whelan\-And\-Goldman 2001 model (amino acid alignments only)
+.HP
+\fB\-quote\fR \fB\-\-\fR allow spaces and other restricted characters (but not ' characters) in
+.IP
+sequence names and quote names in the output tree (fasta input only;
+fasttree will not be able to read these trees back in
+.HP
+\fB\-noml\fR to turn off maximum\-likelihood
+.HP
+\fB\-nome\fR to turn off minimum\-evolution NNIs and SPRs
+.IP
+(recommended if running additional ML NNIs with \fB\-intree\fR)
+.HP
+\fB\-nome\fR \fB\-mllen\fR with \fB\-intree\fR to optimize branch lengths for a fixed topology
+.HP
+\fB\-cat\fR # to specify the number of rate categories of sites (default 20)
+.IP
+or \fB\-nocat\fR to use constant rates
+.HP
+\fB\-gamma\fR \fB\-\-\fR after optimizing the tree under the CAT approximation,
+.IP
+rescale the lengths to optimize the Gamma20 likelihood
+.HP
+\fB\-constraints\fR constraintAlignment to constrain the topology search
+.IP
+constraintAlignment should have 1s or 0s to indicates splits
+.HP
+\fB\-expert\fR \fB\-\-\fR see more options
+.PP
+.SS Detailed usage for fasttree 2.1.4 SSE3:
+fasttree [\-nt] [\-n 100] [\-quote] [\-pseudo | \fB\-pseudo\fR 1.0]
+.IP
+[\-boot 1000 | \fB\-nosupport]\fR
+[\-intree starting_trees_file | \fB\-intree1\fR starting_tree_file]
+[\-quiet | \fB\-nopr]\fR
+[\-nni 10] [\-spr 2] [\-noml | \fB\-mllen\fR | \fB\-mlnni\fR 10]
+[\-mlacc 2] [\-cat 20 | \fB\-nocat]\fR [\-gamma]
+[\-slow | \fB\-fastest]\fR [\-2nd | \fB\-no2nd]\fR [\-slownni] [\-seed 1253]
+[\-top | \fB\-notop]\fR [\-topm 1.0 [\-close 0.75] [\-refresh 0.8]]
+[\-matrix Matrix | \fB\-nomatrix]\fR [\-nj | \fB\-bionj]\fR
+[\-wag] [\-nt] [\-gtr] [\-gtrrates ac ag at cg ct gt] [\-gtrfreq A C G T]
+[ \fB\-constraints\fR constraintAlignment [ \fB\-constraintWeight\fR 100.0 ] ]
+[\-log logfile]
+.IP
+[ alignment_file ]
+.IP
+\f(CW> newick_tree\fR
+.PP
+or
+.PP
+fasttree [\-nt] [\-matrix Matrix | \fB\-nomatrix]\fR [\-rawdist] \fB\-makematrix\fR [alignment]
+.IP
+[\-n 100] > phylip_distance_matrix
+.IP
+fasttree supports fasta or phylip interleaved alignments
+By default fasttree expects protein alignments, use \fB\-nt\fR for nucleotides
+fasttree reads standard input if no alignment file is given
+.SS "Input/output options:"
+.HP
+\fB\-n\fR \fB\-\-\fR read in multiple alignments in. This only
+.IP
+works with phylip interleaved format. For example, you can
+use it with the output from phylip's seqboot. If you use \fB\-n\fR, fasttree
+will write 1 tree per line to standard output.
+.HP
+\fB\-intree\fR newickfile \fB\-\-\fR read the starting tree in from newickfile.
+.IP
+Any branch lengths in the starting trees are ignored.
+.HP
+\fB\-intree\fR with \fB\-n\fR will read a separate starting tree for each alignment.
+.HP
+\fB\-intree1\fR newickfile \fB\-\-\fR read the same starting tree for each alignment
+.HP
+\fB\-quiet\fR \fB\-\-\fR do not write to standard error during normal operation (no progress
+.IP
+indicator, no options summary, no likelihood values, etc.)
+.HP
+\fB\-nopr\fR \fB\-\-\fR do not write the progress indicator to stderr
+.HP
+\fB\-log\fR logfile \fB\-\-\fR save intermediate trees so you can extract
+.IP
+the trees and restart long\-running jobs if they crash
+\fB\-log\fR also reports the per\-site rates (1 means slowest category)
+.HP
+\fB\-quote\fR \fB\-\-\fR quote sequence names in the output and allow spaces, commas,
+.IP
+parentheses, and colons in them but not ' characters (fasta files only)
+.SS "Distances:"
+.IP
+Default: For protein sequences, log\-corrected distances and an
+.IP
+amino acid dissimilarity matrix derived from BLOSUM45
+.IP
+or for nucleotide sequences, Jukes\-Cantor distances
+To specify a different matrix, use \fB\-matrix\fR FilePrefix or \fB\-nomatrix\fR
+Use \fB\-rawdist\fR to turn the log\-correction off
+or to use %different instead of Jukes\-Cantor
+.HP
+\fB\-pseudo\fR [weight] \fB\-\-\fR Use pseudocounts to estimate distances between
+.IP
+sequences with little or no overlap. (Off by default.) Recommended
+if analyzing the alignment has sequences with little or no overlap.
+If the weight is not specified, it is 1.0
+.SS "Topology refinement:"
+.IP
+By default, fasttree tries to improve the tree with up to 4*log2(N)
+rounds of minimum\-evolution nearest\-neighbor interchanges (NNI),
+where N is the number of unique sequences, 2 rounds of
+subtree\-prune\-regraft (SPR) moves (also min. evo.), and
+up to 2*log(N) rounds of maximum\-likelihood NNIs.
+Use \fB\-nni\fR to set the number of rounds of min. evo. NNIs,
+and \fB\-spr\fR to set the rounds of SPRs.
+Use \fB\-noml\fR to turn off both min\-evo NNIs and SPRs (useful if refining
+.IP
+an approximately maximum\-likelihood tree with further NNIs)
+.IP
+Use \fB\-sprlength\fR set the maximum length of a SPR move (default 10)
+Use \fB\-mlnni\fR to set the number of rounds of maximum\-likelihood NNIs
+Use \fB\-mlacc\fR 2 or \fB\-mlacc\fR 3 to always optimize all 5 branches at each NNI,
+.IP
+and to optimize all 5 branches in 2 or 3 rounds
+.IP
+Use \fB\-mllen\fR to optimize branch lengths without ML NNIs
+Use \fB\-mllen\fR \fB\-nome\fR with \fB\-intree\fR to optimize branch lengths on a fixed topology
+Use \fB\-slownni\fR to turn off heuristics to avoid constant subtrees (affects both
+.IP
+ML and ME NNIs)
+.SS "Maximum likelihood model options:"
+.HP
+\fB\-wag\fR \fB\-\-\fR Whelan\-And\-Goldman 2001 model instead of (default) Jones\-Taylor\-Thorton 1992 model (a.a. only)
+.HP
+\fB\-gtr\fR \fB\-\-\fR generalized time\-reversible instead of (default) Jukes\-Cantor (nt only)
+.HP
+\fB\-cat\fR # \fB\-\-\fR specify the number of rate categories of sites (default 20)
+.HP
+\fB\-nocat\fR \fB\-\-\fR no CAT model (just 1 category)
+.HP
+\fB\-gamma\fR \fB\-\-\fR after the final round of optimizing branch lengths with the CAT model,
+.IP
+report the likelihood under the discrete gamma model with the same
+number of categories. fasttree uses the same branch lengths but
+optimizes the gamma shape parameter and the scale of the lengths.
+The final tree will have rescaled lengths. Used with \fB\-log\fR, this
+also generates per\-site likelihoods for use with CONSEL, see
+GammaLogToPaup.pl and documentation on the fasttree web site.
+.SS "Support value options:"
+.IP
+By default, fasttree computes local support values by resampling the site
+likelihoods 1,000 times and the Shimodaira Hasegawa test. If you specify \fB\-nome\fR,
+it will compute minimum\-evolution bootstrap supports instead
+In either case, the support values are proportions ranging from 0 to 1
+.IP
+Use \fB\-nosupport\fR to turn off support values or \fB\-boot\fR 100 to use just 100 resamples
+Use \fB\-seed\fR to initialize the random number generator
+.SS "Searching for the best join:"
+.IP
+By default, fasttree combines the 'visible set' of fast neighbor\-joining with
+.IP
+local hill\-climbing as in relaxed neighbor\-joining
+.HP
+\fB\-slow\fR \fB\-\-\fR exhaustive search (like NJ or BIONJ, but different gap handling)
+.HP
+\fB\-slow\fR takes half an hour instead of 8 seconds for 1,250 proteins
+.HP
+\fB\-fastest\fR \fB\-\-\fR search the visible set (the top hit for each node) only
+.IP
+Unlike the original fast neighbor\-joining, \fB\-fastest\fR updates visible(C)
+after joining A and B if join(AB,C) is better than join(C,visible(C))
+\fB\-fastest\fR also updates out\-distances in a very lazy way,
+\fB\-fastest\fR sets \fB\-2nd\fR on as well, use \fB\-fastest\fR \fB\-no2nd\fR to avoid this
+.SS "Top-hit heuristics:"
+.IP
+By default, fasttree uses a top\-hit list to speed up search
+Use \fB\-notop\fR (or \fB\-slow\fR) to turn this feature off
+.IP
+and compare all leaves to each other,
+and all new joined nodes to each other
+.HP
+\fB\-topm\fR 1.0 \fB\-\-\fR set the top\-hit list size to parameter*sqrt(N)
+.IP
+fasttree estimates the top m hits of a leaf from the
+top 2*m hits of a 'close' neighbor, where close is
+defined as d(seed,close) < 0.75 * d(seed, hit of rank 2*m),
+and updates the top\-hits as joins proceed
+.HP
+\fB\-close\fR 0.75 \fB\-\-\fR modify the close heuristic, lower is more conservative
+.HP
+\fB\-refresh\fR 0.8 \fB\-\-\fR compare a joined node to all other nodes if its
+.IP
+top\-hit list is less than 80% of the desired length,
+or if the age of the top\-hit list is log2(m) or greater
+.HP
+\fB\-2nd\fR or \fB\-no2nd\fR to turn 2nd\-level top hits heuristic on or off
+.IP
+This reduces memory usage and running time but may lead to
+marginal reductions in tree quality.
+(By default, \fB\-fastest\fR turns on \fB\-2nd\fR.)
+.SS "Join options:"
+.HP
+\fB\-nj\fR: regular (unweighted) neighbor\-joining (default)
+.HP
+\fB\-bionj\fR: weighted joins as in BIONJ
+.IP
+fasttree will also weight joins during NNIs
+.SS "Constrained topology search options:"
+.HP
+\fB\-constraints\fR alignmentfile \fB\-\-\fR an alignment with values of 0, 1, and \-
+.IP
+Not all sequences need be present. A column of 0s and 1s defines a
+constrained split. Some constraints may be violated
+(see 'violating constraints:' in standard error).
+.HP
+\fB\-constraintWeight\fR \fB\-\-\fR how strongly to weight the constraints. A value of 1
+.IP
+means a penalty of 1 in tree length for violating a constraint
+Default: 100.0
+.PP
+For more information, see http://www.microbesonline.org/fasttree/
+.IP
+or the comments in the source code
+.IP
+fasttree protein_alignment > tree
+fasttree \fB\-nt\fR nucleotide_alignment > tree
+fasttree \fB\-nt\fR \fB\-gtr\fR < nucleotide_alignment > tree
+.PP
+fasttree accepts alignments in fasta or phylip interleaved formats
+.SS "Common options (must be before the alignment file):"
+.HP
+\fB\-quiet\fR to suppress reporting information
+.HP
+\fB\-nopr\fR to suppress progress indicator
+.HP
+\fB\-log\fR logfile \fB\-\-\fR save intermediate trees, settings, and model details
+.HP
+\fB\-fastest\fR \fB\-\-\fR speed up the neighbor joining phase & reduce memory usage
+.IP
+(recommended for >50,000 sequences)
+.HP
+\fB\-n\fR <number> to analyze multiple alignments (phylip format only)
+.IP
+(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
+.HP
+\fB\-nosupport\fR to not compute support values
+.HP
+\fB\-intree\fR newick_file to set the starting tree(s)
+.HP
+\fB\-intree1\fR newick_file to use this starting tree for all the alignments
+.IP
+(for faster global bootstrap on huge alignments)
+.HP
+\fB\-pseudo\fR to use pseudocounts (recommended for highly gapped sequences)
+.HP
+\fB\-gtr\fR \fB\-\-\fR generalized time\-reversible model (nucleotide alignments only)
+.HP
+\fB\-wag\fR \fB\-\-\fR Whelan\-And\-Goldman 2001 model (amino acid alignments only)
+.HP
+\fB\-quote\fR \fB\-\-\fR allow spaces and other restricted characters (but not ' characters) in
+.IP
+sequence names and quote names in the output tree (fasta input only;
+fasttree will not be able to read these trees back in
+.HP
+\fB\-noml\fR to turn off maximum\-likelihood
+.HP
+\fB\-nome\fR to turn off minimum\-evolution NNIs and SPRs
+.IP
+(recommended if running additional ML NNIs with \fB\-intree\fR)
+.HP
+\fB\-nome\fR \fB\-mllen\fR with \fB\-intree\fR to optimize branch lengths for a fixed topology
+.HP
+\fB\-cat\fR # to specify the number of rate categories of sites (default 20)
+.IP
+or \fB\-nocat\fR to use constant rates
+.HP
+\fB\-gamma\fR \fB\-\-\fR after optimizing the tree under the CAT approximation,
+.IP
+rescale the lengths to optimize the Gamma20 likelihood
+.HP
+\fB\-constraints\fR constraintAlignment to constrain the topology search
+.IP
+constraintAlignment should have 1s or 0s to indicates splits
+.HP
+\fB\-expert\fR \fB\-\-\fR see more options
+.PP
+For more information, see http://www.microbesonline.org/fasttree/
Modified: trunk/packages/fasttree/trunk/debian/fasttree.install
===================================================================
--- trunk/packages/fasttree/trunk/debian/fasttree.install 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/fasttree.install 2012-06-15 18:05:04 UTC (rev 11357)
@@ -1 +1,2 @@
fasttree usr/bin
+fasttreeMP usr/bin
Added: trunk/packages/fasttree/trunk/debian/fasttree.upstream-metadata.yaml
===================================================================
--- trunk/packages/fasttree/trunk/debian/fasttree.upstream-metadata.yaml (rev 0)
+++ trunk/packages/fasttree/trunk/debian/fasttree.upstream-metadata.yaml 2012-06-15 18:05:04 UTC (rev 11357)
@@ -0,0 +1,16 @@
+Contact: fasttree at microbesonline.org.
+DOI: 10.1371/journal.pone.0009490
+Homepage: http://www.microbesonline.org/fasttree/
+Name: FastTree
+Reference:
+ author: Price, Morgan N. AND Dehal, Paramvir S. AND Arkin, Adam P.
+ journal: PLoS ONE
+ publisher: Public Library of Science
+ title: FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments.
+ year: 2010
+ month: 03
+ volume: 5
+ url: http://dx.doi.org/10.1371%2Fjournal.pone.0009490
+ pages: e9490
+ number: 3
+Watch: http://www.microbesonline.org/fasttree/FastTree-(.*)\.c
Added: trunk/packages/fasttree/trunk/debian/fasttreeMP.1
===================================================================
--- trunk/packages/fasttree/trunk/debian/fasttreeMP.1 (rev 0)
+++ trunk/packages/fasttree/trunk/debian/fasttreeMP.1 2012-06-15 18:05:04 UTC (rev 11357)
@@ -0,0 +1,339 @@
+.TH "fasttreeMP" "1" "June 2012" "Lawrence Berkeley National Lab" "User Commands"
+.SH NAME
+fasttreeMP \- create phylogenetic trees from alignments of nucleotide or protein sequences (openMP version)
+.SH DESCRIPTION
+fasttreeMP infers approximately-maximum-likelihood phylogenetic trees from
+alignments of nucleotide or protein sequences. It handles alignments
+with up to a million of sequences in a reasonable amount of time and memory.
+
+fasttreeMP is more accurate than PhyML 3 with default settings, and much
+more accurate than the distance-matrix methods that are traditionally
+used for large alignments. fasttreeMP uses the Jukes-Cantor or generalized
+time-reversible (GTR) models of nucleotide evolution and the JTT
+(Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
+for the varying rates of evolution across sites, fasttreeMP uses a single
+rate for each site (the "CAT" approximation). To quickly estimate the
+reliability of each split in the tree, fasttreeMP computes local support
+values with the Shimodaira-Hasegawa test (these are the same as PhyML
+3's "SH-like local supports").
+.SH SYNOPSIS
+.PP
+.B fasttreeMP protein_alignment > tree
+.PP
+.B fasttreeMP \fB\-nt\fR nucleotide_alignment > tree
+.PP
+.B fasttreeMP \fB\-nt\fR \fB\-gtr\fR < nucleotide_alignment > tree
+.PP
+fasttreeMP accepts alignments in fasta or phylip interleaved formats
+.SS "Common options (must be before the alignment file):"
+.HP
+\fB\-quiet\fR to suppress reporting information
+.HP
+\fB\-nopr\fR to suppress progress indicator
+.HP
+\fB\-log\fR logfile \fB\-\-\fR save intermediate trees, settings, and model details
+.HP
+\fB\-fastest\fR \fB\-\-\fR speed up the neighbor joining phase & reduce memory usage
+.IP
+(recommended for >50,000 sequences)
+.HP
+\fB\-n\fR <number> to analyze multiple alignments (phylip format only)
+.IP
+(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
+.HP
+\fB\-nosupport\fR to not compute support values
+.HP
+\fB\-intree\fR newick_file to set the starting tree(s)
+.HP
+\fB\-intree1\fR newick_file to use this starting tree for all the alignments
+.IP
+(for faster global bootstrap on huge alignments)
+.HP
+\fB\-pseudo\fR to use pseudocounts (recommended for highly gapped sequences)
+.HP
+\fB\-gtr\fR \fB\-\-\fR generalized time\-reversible model (nucleotide alignments only)
+.HP
+\fB\-wag\fR \fB\-\-\fR Whelan\-And\-Goldman 2001 model (amino acid alignments only)
+.HP
+\fB\-quote\fR \fB\-\-\fR allow spaces and other restricted characters (but not ' characters) in
+.IP
+sequence names and quote names in the output tree (fasta input only;
+fasttreeMP will not be able to read these trees back in
+.HP
+\fB\-noml\fR to turn off maximum\-likelihood
+.HP
+\fB\-nome\fR to turn off minimum\-evolution NNIs and SPRs
+.IP
+(recommended if running additional ML NNIs with \fB\-intree\fR)
+.HP
+\fB\-nome\fR \fB\-mllen\fR with \fB\-intree\fR to optimize branch lengths for a fixed topology
+.HP
+\fB\-cat\fR # to specify the number of rate categories of sites (default 20)
+.IP
+or \fB\-nocat\fR to use constant rates
+.HP
+\fB\-gamma\fR \fB\-\-\fR after optimizing the tree under the CAT approximation,
+.IP
+rescale the lengths to optimize the Gamma20 likelihood
+.HP
+\fB\-constraints\fR constraintAlignment to constrain the topology search
+.IP
+constraintAlignment should have 1s or 0s to indicates splits
+.HP
+\fB\-expert\fR \fB\-\-\fR see more options
+.PP
+.SS Detailed usage for fasttreeMP 2.1.4 SSE3:
+fasttreeMP [\-nt] [\-n 100] [\-quote] [\-pseudo | \fB\-pseudo\fR 1.0]
+.IP
+[\-boot 1000 | \fB\-nosupport]\fR
+[\-intree starting_trees_file | \fB\-intree1\fR starting_tree_file]
+[\-quiet | \fB\-nopr]\fR
+[\-nni 10] [\-spr 2] [\-noml | \fB\-mllen\fR | \fB\-mlnni\fR 10]
+[\-mlacc 2] [\-cat 20 | \fB\-nocat]\fR [\-gamma]
+[\-slow | \fB\-fastest]\fR [\-2nd | \fB\-no2nd]\fR [\-slownni] [\-seed 1253]
+[\-top | \fB\-notop]\fR [\-topm 1.0 [\-close 0.75] [\-refresh 0.8]]
+[\-matrix Matrix | \fB\-nomatrix]\fR [\-nj | \fB\-bionj]\fR
+[\-wag] [\-nt] [\-gtr] [\-gtrrates ac ag at cg ct gt] [\-gtrfreq A C G T]
+[ \fB\-constraints\fR constraintAlignment [ \fB\-constraintWeight\fR 100.0 ] ]
+[\-log logfile]
+.IP
+[ alignment_file ]
+.IP
+\f(CW> newick_tree\fR
+.PP
+or
+.PP
+fasttreeMP [\-nt] [\-matrix Matrix | \fB\-nomatrix]\fR [\-rawdist] \fB\-makematrix\fR [alignment]
+.IP
+[\-n 100] > phylip_distance_matrix
+.IP
+fasttreeMP supports fasta or phylip interleaved alignments
+By default fasttreeMP expects protein alignments, use \fB\-nt\fR for nucleotides
+fasttreeMP reads standard input if no alignment file is given
+.SS "Input/output options:"
+.HP
+\fB\-n\fR \fB\-\-\fR read in multiple alignments in. This only
+.IP
+works with phylip interleaved format. For example, you can
+use it with the output from phylip's seqboot. If you use \fB\-n\fR, fasttreeMP
+will write 1 tree per line to standard output.
+.HP
+\fB\-intree\fR newickfile \fB\-\-\fR read the starting tree in from newickfile.
+.IP
+Any branch lengths in the starting trees are ignored.
+.HP
+\fB\-intree\fR with \fB\-n\fR will read a separate starting tree for each alignment.
+.HP
+\fB\-intree1\fR newickfile \fB\-\-\fR read the same starting tree for each alignment
+.HP
+\fB\-quiet\fR \fB\-\-\fR do not write to standard error during normal operation (no progress
+.IP
+indicator, no options summary, no likelihood values, etc.)
+.HP
+\fB\-nopr\fR \fB\-\-\fR do not write the progress indicator to stderr
+.HP
+\fB\-log\fR logfile \fB\-\-\fR save intermediate trees so you can extract
+.IP
+the trees and restart long\-running jobs if they crash
+\fB\-log\fR also reports the per\-site rates (1 means slowest category)
+.HP
+\fB\-quote\fR \fB\-\-\fR quote sequence names in the output and allow spaces, commas,
+.IP
+parentheses, and colons in them but not ' characters (fasta files only)
+.SS "Distances:"
+.IP
+Default: For protein sequences, log\-corrected distances and an
+.IP
+amino acid dissimilarity matrix derived from BLOSUM45
+.IP
+or for nucleotide sequences, Jukes\-Cantor distances
+To specify a different matrix, use \fB\-matrix\fR FilePrefix or \fB\-nomatrix\fR
+Use \fB\-rawdist\fR to turn the log\-correction off
+or to use %different instead of Jukes\-Cantor
+.HP
+\fB\-pseudo\fR [weight] \fB\-\-\fR Use pseudocounts to estimate distances between
+.IP
+sequences with little or no overlap. (Off by default.) Recommended
+if analyzing the alignment has sequences with little or no overlap.
+If the weight is not specified, it is 1.0
+.SS "Topology refinement:"
+.IP
+By default, fasttreeMP tries to improve the tree with up to 4*log2(N)
+rounds of minimum\-evolution nearest\-neighbor interchanges (NNI),
+where N is the number of unique sequences, 2 rounds of
+subtree\-prune\-regraft (SPR) moves (also min. evo.), and
+up to 2*log(N) rounds of maximum\-likelihood NNIs.
+Use \fB\-nni\fR to set the number of rounds of min. evo. NNIs,
+and \fB\-spr\fR to set the rounds of SPRs.
+Use \fB\-noml\fR to turn off both min\-evo NNIs and SPRs (useful if refining
+.IP
+an approximately maximum\-likelihood tree with further NNIs)
+.IP
+Use \fB\-sprlength\fR set the maximum length of a SPR move (default 10)
+Use \fB\-mlnni\fR to set the number of rounds of maximum\-likelihood NNIs
+Use \fB\-mlacc\fR 2 or \fB\-mlacc\fR 3 to always optimize all 5 branches at each NNI,
+.IP
+and to optimize all 5 branches in 2 or 3 rounds
+.IP
+Use \fB\-mllen\fR to optimize branch lengths without ML NNIs
+Use \fB\-mllen\fR \fB\-nome\fR with \fB\-intree\fR to optimize branch lengths on a fixed topology
+Use \fB\-slownni\fR to turn off heuristics to avoid constant subtrees (affects both
+.IP
+ML and ME NNIs)
+.SS "Maximum likelihood model options:"
+.HP
+\fB\-wag\fR \fB\-\-\fR Whelan\-And\-Goldman 2001 model instead of (default) Jones\-Taylor\-Thorton 1992 model (a.a. only)
+.HP
+\fB\-gtr\fR \fB\-\-\fR generalized time\-reversible instead of (default) Jukes\-Cantor (nt only)
+.HP
+\fB\-cat\fR # \fB\-\-\fR specify the number of rate categories of sites (default 20)
+.HP
+\fB\-nocat\fR \fB\-\-\fR no CAT model (just 1 category)
+.HP
+\fB\-gamma\fR \fB\-\-\fR after the final round of optimizing branch lengths with the CAT model,
+.IP
+report the likelihood under the discrete gamma model with the same
+number of categories. fasttreeMP uses the same branch lengths but
+optimizes the gamma shape parameter and the scale of the lengths.
+The final tree will have rescaled lengths. Used with \fB\-log\fR, this
+also generates per\-site likelihoods for use with CONSEL, see
+GammaLogToPaup.pl and documentation on the fasttreeMP web site.
+.SS "Support value options:"
+.IP
+By default, fasttreeMP computes local support values by resampling the site
+likelihoods 1,000 times and the Shimodaira Hasegawa test. If you specify \fB\-nome\fR,
+it will compute minimum\-evolution bootstrap supports instead
+In either case, the support values are proportions ranging from 0 to 1
+.IP
+Use \fB\-nosupport\fR to turn off support values or \fB\-boot\fR 100 to use just 100 resamples
+Use \fB\-seed\fR to initialize the random number generator
+.SS "Searching for the best join:"
+.IP
+By default, fasttreeMP combines the 'visible set' of fast neighbor\-joining with
+.IP
+local hill\-climbing as in relaxed neighbor\-joining
+.HP
+\fB\-slow\fR \fB\-\-\fR exhaustive search (like NJ or BIONJ, but different gap handling)
+.HP
+\fB\-slow\fR takes half an hour instead of 8 seconds for 1,250 proteins
+.HP
+\fB\-fastest\fR \fB\-\-\fR search the visible set (the top hit for each node) only
+.IP
+Unlike the original fast neighbor\-joining, \fB\-fastest\fR updates visible(C)
+after joining A and B if join(AB,C) is better than join(C,visible(C))
+\fB\-fastest\fR also updates out\-distances in a very lazy way,
+\fB\-fastest\fR sets \fB\-2nd\fR on as well, use \fB\-fastest\fR \fB\-no2nd\fR to avoid this
+.SS "Top-hit heuristics:"
+.IP
+By default, fasttreeMP uses a top\-hit list to speed up search
+Use \fB\-notop\fR (or \fB\-slow\fR) to turn this feature off
+.IP
+and compare all leaves to each other,
+and all new joined nodes to each other
+.HP
+\fB\-topm\fR 1.0 \fB\-\-\fR set the top\-hit list size to parameter*sqrt(N)
+.IP
+fasttreeMP estimates the top m hits of a leaf from the
+top 2*m hits of a 'close' neighbor, where close is
+defined as d(seed,close) < 0.75 * d(seed, hit of rank 2*m),
+and updates the top\-hits as joins proceed
+.HP
+\fB\-close\fR 0.75 \fB\-\-\fR modify the close heuristic, lower is more conservative
+.HP
+\fB\-refresh\fR 0.8 \fB\-\-\fR compare a joined node to all other nodes if its
+.IP
+top\-hit list is less than 80% of the desired length,
+or if the age of the top\-hit list is log2(m) or greater
+.HP
+\fB\-2nd\fR or \fB\-no2nd\fR to turn 2nd\-level top hits heuristic on or off
+.IP
+This reduces memory usage and running time but may lead to
+marginal reductions in tree quality.
+(By default, \fB\-fastest\fR turns on \fB\-2nd\fR.)
+.SS "Join options:"
+.HP
+\fB\-nj\fR: regular (unweighted) neighbor\-joining (default)
+.HP
+\fB\-bionj\fR: weighted joins as in BIONJ
+.IP
+fasttreeMP will also weight joins during NNIs
+.SS "Constrained topology search options:"
+.HP
+\fB\-constraints\fR alignmentfile \fB\-\-\fR an alignment with values of 0, 1, and \-
+.IP
+Not all sequences need be present. A column of 0s and 1s defines a
+constrained split. Some constraints may be violated
+(see 'violating constraints:' in standard error).
+.HP
+\fB\-constraintWeight\fR \fB\-\-\fR how strongly to weight the constraints. A value of 1
+.IP
+means a penalty of 1 in tree length for violating a constraint
+Default: 100.0
+.PP
+For more information, see http://www.microbesonline.org/fasttree/
+.IP
+or the comments in the source code
+.IP
+fasttreeMP protein_alignment > tree
+fasttreeMP \fB\-nt\fR nucleotide_alignment > tree
+fasttreeMP \fB\-nt\fR \fB\-gtr\fR < nucleotide_alignment > tree
+.PP
+fasttreeMP accepts alignments in fasta or phylip interleaved formats
+.SS "Common options (must be before the alignment file):"
+.HP
+\fB\-quiet\fR to suppress reporting information
+.HP
+\fB\-nopr\fR to suppress progress indicator
+.HP
+\fB\-log\fR logfile \fB\-\-\fR save intermediate trees, settings, and model details
+.HP
+\fB\-fastest\fR \fB\-\-\fR speed up the neighbor joining phase & reduce memory usage
+.IP
+(recommended for >50,000 sequences)
+.HP
+\fB\-n\fR <number> to analyze multiple alignments (phylip format only)
+.IP
+(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
+.HP
+\fB\-nosupport\fR to not compute support values
+.HP
+\fB\-intree\fR newick_file to set the starting tree(s)
+.HP
+\fB\-intree1\fR newick_file to use this starting tree for all the alignments
+.IP
+(for faster global bootstrap on huge alignments)
+.HP
+\fB\-pseudo\fR to use pseudocounts (recommended for highly gapped sequences)
+.HP
+\fB\-gtr\fR \fB\-\-\fR generalized time\-reversible model (nucleotide alignments only)
+.HP
+\fB\-wag\fR \fB\-\-\fR Whelan\-And\-Goldman 2001 model (amino acid alignments only)
+.HP
+\fB\-quote\fR \fB\-\-\fR allow spaces and other restricted characters (but not ' characters) in
+.IP
+sequence names and quote names in the output tree (fasta input only;
+fasttreeMP will not be able to read these trees back in
+.HP
+\fB\-noml\fR to turn off maximum\-likelihood
+.HP
+\fB\-nome\fR to turn off minimum\-evolution NNIs and SPRs
+.IP
+(recommended if running additional ML NNIs with \fB\-intree\fR)
+.HP
+\fB\-nome\fR \fB\-mllen\fR with \fB\-intree\fR to optimize branch lengths for a fixed topology
+.HP
+\fB\-cat\fR # to specify the number of rate categories of sites (default 20)
+.IP
+or \fB\-nocat\fR to use constant rates
+.HP
+\fB\-gamma\fR \fB\-\-\fR after optimizing the tree under the CAT approximation,
+.IP
+rescale the lengths to optimize the Gamma20 likelihood
+.HP
+\fB\-constraints\fR constraintAlignment to constrain the topology search
+.IP
+constraintAlignment should have 1s or 0s to indicates splits
+.HP
+\fB\-expert\fR \fB\-\-\fR see more options
+.PP
+For more information, see http://www.microbesonline.org/fasttree/
Added: trunk/packages/fasttree/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/fasttree/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/fasttree/trunk/debian/get-orig-source 2012-06-15 18:05:04 UTC (rev 11357)
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | cut -d- -f1`
+
+
+mkdir -p ../tarballs
+uscan --verbose --force-download --repack --destdir=../tarballs
+cd ../tarballs
+/usr/bin/wget http://www.microbesonline.org/fasttree/ChangeLog
+rm *.orig.tar.gz
+for f in FastTree*.c; do
+ dir=`echo $f|sed "s/\.c//"`
+ tarfile=`echo $f|sed "s/c/tar.gz/"`
+ mkdir $dir
+ mv $f $dir/fasttree.c
+ cp ChangeLog $dir/changelog
+ tar -czf $tarfile $dir
+ rm -rf $dir
+done
+rm ChangeLog
+ln -s $tarfile ${PKG}_${VERSION}.orig.tar.gz
Property changes on: trunk/packages/fasttree/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/fasttree/trunk/debian/manpages
===================================================================
--- trunk/packages/fasttree/trunk/debian/manpages (rev 0)
+++ trunk/packages/fasttree/trunk/debian/manpages 2012-06-15 18:05:04 UTC (rev 11357)
@@ -0,0 +1,2 @@
+debian/fasttree.1
+debian/fasttreeMP.1
Modified: trunk/packages/fasttree/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/fasttree/trunk/debian/patches/Makefile.patch 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/patches/Makefile.patch 2012-06-15 18:05:04 UTC (rev 11357)
@@ -1,3 +1,5 @@
+Description: As the original source is just a c-file, the Makefile
+ needs to be created.
Index: fasttree-2.1.0.c/Makefile
===================================================================
--- /dev/null 1970-01-01 00:00:00.000000000 +0000
@@ -2,7 +4,12 @@
+++ fasttree-2.1.0.c/Makefile 2011-03-02 19:07:11.000000000 +0100
-@@ -0,0 +1,6 @@
+@@ -0,0 +1,11 @@
+
++all: fasttree fasttreeMP
++
+fasttree: fasttree.c
-+ $(CC) $(CFLAGS) -o $@ $< -lm
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< -lm
+
++fasttreeMP: fasttree.c
++ $(CC) -DOPENMP -fopenmp $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< -lm
++
+distclean clean:
Modified: trunk/packages/fasttree/trunk/debian/rules
===================================================================
--- trunk/packages/fasttree/trunk/debian/rules 2012-06-15 14:31:56 UTC (rev 11356)
+++ trunk/packages/fasttree/trunk/debian/rules 2012-06-15 18:05:04 UTC (rev 11357)
@@ -11,3 +11,7 @@
%:
dh $@
+
+get-orig-source:
+ ./debian/get-orig-source
+
Added: trunk/packages/fasttree/trunk/debian/watch
===================================================================
--- trunk/packages/fasttree/trunk/debian/watch (rev 0)
+++ trunk/packages/fasttree/trunk/debian/watch 2012-06-15 18:05:04 UTC (rev 11357)
@@ -0,0 +1,2 @@
+version=3
+http://www.microbesonline.org/fasttree/FastTree-(.*)\.c
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