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 <moel...@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 <moel...@debian.org> Wed, 02 Mar 2011 18:52:56 +0100 + -- Thorsten Alteholz <deb...@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-packag...@lists.alioth.debian.org> DM-Upload-Allowed: yes -Uploaders: Steffen Moeller <moel...@debian.org> -Build-Depends: debhelper (>= 7.0.50~) -Standards-Version: 3.9.1 +Uploaders: Steffen Moeller <moel...@debian.org>, + Thorsten Alteholz <deb...@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 <moel...@debian.org> + 2012 Thorsten Alteholz <deb...@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: fastt...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit