[med-svn] r4100 - trunk/packages/seqan/trunk/debian
Soeren Sonnenburg
sonne at alioth.debian.org
Wed Sep 30 21:00:42 UTC 2009
Author: sonne
Date: 2009-09-30 21:00:40 +0000 (Wed, 30 Sep 2009)
New Revision: 4100
Added:
trunk/packages/seqan/trunk/debian/dfi.1
trunk/packages/seqan/trunk/debian/micro_razers.1
trunk/packages/seqan/trunk/debian/pair_align.1
trunk/packages/seqan/trunk/debian/razers.1
trunk/packages/seqan/trunk/debian/seqan_tcoffee.1
trunk/packages/seqan/trunk/debian/seqcons.1
trunk/packages/seqan/trunk/debian/tree_recon.1
Modified:
trunk/packages/seqan/trunk/debian/control
trunk/packages/seqan/trunk/debian/orig-tar.sh
trunk/packages/seqan/trunk/debian/rules
Log:
build apps and add man pages
Modified: trunk/packages/seqan/trunk/debian/control
===================================================================
--- trunk/packages/seqan/trunk/debian/control 2009-09-30 19:23:13 UTC (rev 4099)
+++ trunk/packages/seqan/trunk/debian/control 2009-09-30 21:00:40 UTC (rev 4100)
@@ -11,7 +11,7 @@
Package: seqan-apps
Section: libdevel
-Architecture: all
+Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: A C++ template library for the analysis of sequences.
SeqAn is a C++ template library of efficient algorithms and data
Added: trunk/packages/seqan/trunk/debian/dfi.1
===================================================================
--- trunk/packages/seqan/trunk/debian/dfi.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/dfi.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,44 @@
+.TH DFI "1" "September 2009" "DFI version 2.0 20090715 [4670]" "User Commands"
+.SH NAME
+DFI \- manual page for DFI version 2.0 20090715 [4670]
+.SH SYNOPSIS
+.B dfi
+[\fIOPTION\fR]... \fI--minmax <min_1> <max_1> <database 1> \fR... \fI--minmax <min_m> <max_m> <database m>\fR
+.SH DESCRIPTION
+DFI \- The Deferred Frequency Index
+.TP
+dfi [OPTION]... \fB\-\-growth\fR <rho_s> <rho_g> <database 1> <database 2>
+.TP
+dfi [OPTION]... \fB\-\-entropy\fR <rho_s> <alpha> <database 1> <database 2> ... <database m>
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+displays this help message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version information
+.TP
+\fB\-f\fR, \fB\-\-minmax\fR NUM1 NUM2
+solve Frequent Pattern Mining Problem
+.TP
+\fB\-g\fR, \fB\-\-growth\fR NUM1 NUM2
+solve Emerging Substring Mining Problem
+.TP
+\fB\-e\fR, \fB\-\-entropy\fR NUM1 NUM2
+solve Entropy Mining Problem
+.TP
+\fB\-p\fR, \fB\-\-protein\fR
+use AminoAcid alphabet (for proteomes)
+.TP
+\fB\-d\fR, \fB\-\-dna\fR
+use DNA alphabet (for genomes)
+.TP
+\fB\-m\fR, \fB\-\-maximal\fR
+output only left and right maximal substrings
+The default is byte alphabet
+.SH AUTHOR
+.br
+dfi was written by David Weese and Marcel H. Schulz.
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
Added: trunk/packages/seqan/trunk/debian/micro_razers.1
===================================================================
--- trunk/packages/seqan/trunk/debian/micro_razers.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/micro_razers.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,82 @@
+.TH MICRORAZERS "1" "September 2009" "MicroRazerS version 0.1 20090710 (prerelease)" "User Commands"
+.SH NAME
+MicroRazerS \- manual page for MicroRazerS version 0.1 20090710 (prerelease)
+.SH SYNOPSIS
+.B micro_razers
+[\fIOPTION\fR]... \fI<GENOME FILE> <READS FILE>\fR
+.SH DESCRIPTION
+MicroRazerS \- Rapid Alignment of Small RNA Reads
+.SS "Main Options:"
+.TP
+\fB\-o\fR, \fB\-\-output\fR FILE
+change output filename (default <READS FILE>.result)
+.TP
+\fB\-sL\fR, \fB\-\-seed\-length\fR NUM
+seed length (default 16)
+.TP
+\fB\-sE\fR, \fB\-\-seed\-error\fR
+allow for one error in the seed (default off)
+.TP
+\fB\-rr\fR, \fB\-\-recognition\-rate\fR
+set lower bound of sensitivity level for one\-error matches (default 100)
+.TP
+\fB\-f\fR, \fB\-\-forward\fR
+only compute forward matches
+.TP
+\fB\-r\fR, \fB\-\-reverse\fR
+only compute reverse complement matches
+.TP
+\fB\-mN\fR, \fB\-\-match\-N\fR
+\&'N' matches with all other characters
+.TP
+\fB\-m\fR, \fB\-\-max\-hits\fR NUM
+output only NUM of the best hits (default 100)
+.TP
+\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
+purge reads with more than max\-hits best matches
+.TP
+\fB\-lm\fR, \fB\-\-low\-memory\fR
+may decrease memory usage at the expense of runtime
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+verbose mode
+.TP
+\fB\-vv\fR, \fB\-\-vverbose\fR
+very verbose mode
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version number
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+print this help
+.SS "Output Format Options:"
+.TP
+\fB\-a\fR, \fB\-\-alignment\fR
+dump the alignment for each match
+.TP
+\fB\-gn\fR, \fB\-\-genome\-naming\fR NUM
+select how genomes are named
+0 = use Fasta id (default)
+1 = enumerate beginning with 1
+.TP
+\fB\-rn\fR, \fB\-\-read\-naming\fR NUM
+select how reads are named
+0 = use Fasta id (default)
+1 = enumerate beginning with 1
+2 = use the read sequence (only for short reads!)
+.TP
+\fB\-so\fR, \fB\-\-sort\-order\fR NUM
+select how matches are sorted
+0 = 1. read number, 2. genome position (default)
+1 = 1. genome position, 2. read number
+.TP
+\fB\-pf\fR, \fB\-\-position\-format\fR
+0 = gap space (default)
+1 = position space
+.SH AUTHOR
+.br
+MicroRazerSwas written by Anne-Katrin Emde.
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
Modified: trunk/packages/seqan/trunk/debian/orig-tar.sh
===================================================================
--- trunk/packages/seqan/trunk/debian/orig-tar.sh 2009-09-30 19:23:13 UTC (rev 4099)
+++ trunk/packages/seqan/trunk/debian/orig-tar.sh 2009-09-30 21:00:40 UTC (rev 4100)
@@ -1,7 +1,7 @@
#!/bin/sh
SEQANDIR=seqan-$2
-SEQANFILE=seqan-${2}.orig.tar.gz
+SEQANFILE=seqan_${2}.orig.tar.gz
# called by uscan with '--upstream-version' <version> <file>
mkdir $SEQANDIR
Added: trunk/packages/seqan/trunk/debian/pair_align.1
===================================================================
--- trunk/packages/seqan/trunk/debian/pair_align.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/pair_align.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,73 @@
+.TH PAIRALIGN "1" "September 2009" "Version 1.0 (15. July 2009) Revision: 4566" "User Commands"
+.SH NAME
+pair_align \- manual page for pair_align 1.0 (15. July 2009) Revision: 4566
+.SH SYNOPSIS
+.B pair_align
+\fI-s <FASTA sequence file> \fR[\fIOptions\fR]
+.SH DESCRIPTION
+Pairwise alignment \- PairAlign
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+displays this help message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version information
+.SS "Main Options:"
+.TP
+\fB\-s\fR, \fB\-\-seq\fR <FASTA Sequence File>
+file with 2 sequences
+.TP
+\fB\-a\fR, \fB\-\-alphabet\fR [protein | dna | rna]
+sequence alphabet (default protein)
+.TP
+\fB\-m\fR, \fB\-\-method\fR [nw, gotoh, sw, lcs]
+alignment method (default gotoh)
+nw = Needleman\-Wunsch
+gotoh = Gotoh
+sw = Smith\-Waterman
+lcs = Longest common subsequence
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <Filename>
+output filename (default out.fasta)
+.TP
+\fB\-f\fR, \fB\-\-format\fR [fasta | msf]
+output format (default fasta)
+.SS "Scoring Options:"
+.TP
+\fB\-g\fR, \fB\-\-gop\fR <Int>
+gap open penalty (default \fB\-11\fR)
+.TP
+\fB\-e\fR, \fB\-\-gex\fR <Int>
+gap extension penalty (default \fB\-1\fR)
+.TP
+\fB\-ma\fR, \fB\-\-matrix\fR <Matrix file>
+score matrix (default Blosum62)
+.TP
+\fB\-ms\fR, \fB\-\-msc\fR <Int>
+match score (default 5)
+.TP
+\fB\-mm\fR, \fB\-\-mmsc\fR <Int>
+mismatch penalty (default \fB\-4\fR)
+.SS "Banded Alignment Options:"
+.TP
+\fB\-lo\fR, \fB\-\-low\fR <Int>
+lower diagonal
+.TP
+\fB\-hi\fR, \fB\-\-high\fR <Int>
+upper diagonal
+.SS "DP Matrix Configuration Options:"
+.TP
+\fB\-c\fR, \fB\-\-config\fR [ffff | ... | tttt]
+alignment configuration (default ffff)
+tfff = First row with 0's
+ftff = First column with 0's
+fftf = Search last column for max
+ffft = Search last row for max
+All combinations are allowed.
+.SH AUTHOR
+.br
+pair_align was written by Tobias Rausch.
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
Added: trunk/packages/seqan/trunk/debian/razers.1
===================================================================
--- trunk/packages/seqan/trunk/debian/razers.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/razers.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,128 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36.
+.TH RAZERS "1" "September 2009" "RazerS version 1.0 20090710 [4739]" "User Commands"
+.SH NAME
+RazerS \- manual page for RazerS version 1.0 20090710 [4739]
+.SH SYNOPSIS
+.B razers
+[\fIOPTION\fR]... \fI<GENOME FILE> <READS FILE>\fR
+.SH DESCRIPTION
+RazerS \- Fast Read Mapping with Sensitivity Control
+.IP
+razers [OPTION]... <GENOME FILE> <MP\-READS FILE1> <MP\-READS FILE2>
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+displays this help message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version information
+.SS "Main Options:"
+.TP
+\fB\-f\fR, \fB\-\-forward\fR
+only compute forward matches
+.TP
+\fB\-r\fR, \fB\-\-reverse\fR
+only compute reverse complement matches
+.TP
+\fB\-i\fR, \fB\-\-percent\-identity\fR NUM
+set the percent identity threshold (default 92)
+.TP
+\fB\-rr\fR, \fB\-\-recognition\-rate\fR NUM
+set the percent recognition rate (default 99)
+.TP
+\fB\-pd\fR, \fB\-\-param\-dir\fR DIR
+folder containing user\-computed parameter files (optional)
+.TP
+\fB\-id\fR, \fB\-\-indels\fR
+allow indels (default: mismatches only)
+.TP
+\fB\-ll\fR, \fB\-\-library\-length\fR NUM
+mate\-pair library length (default 220)
+.TP
+\fB\-le\fR, \fB\-\-library\-error\fR NUM
+mate\-pair library length tolerance (default 50)
+.TP
+\fB\-m\fR, \fB\-\-max\-hits\fR NUM
+output only NUM of the best hits (default 100)
+.TP
+\fB\-\-unique\fR
+output only unique best matches (\fB\-m\fR 1 \fB\-dr\fR 0 \fB\-pa\fR)
+.TP
+\fB\-tr\fR, \fB\-\-trim\-reads\fR NUM
+trim reads to given length (default off)
+.TP
+\fB\-o\fR, \fB\-\-output\fR FILE
+change output filename (default <READS FILE>.result)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+verbose mode
+.TP
+\fB\-vv\fR, \fB\-\-vverbose\fR
+very verbose mode
+.SS "Output Format Options:"
+.TP
+\fB\-a\fR, \fB\-\-alignment\fR
+dump the alignment for each match
+.TP
+\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
+purge reads with more than max\-hits best matches
+.TP
+\fB\-dr\fR, \fB\-\-distance\-range\fR NUM
+only consider matches with at most NUM more errors compared to the best (default output all)
+.TP
+\fB\-of\fR, \fB\-\-output\-format\fR NUM
+set output format (default 0)
+0 = Razer format
+1 = enhanced Fasta format
+2 = Eland format
+3 = GFF format
+.TP
+\fB\-gn\fR, \fB\-\-genome\-naming\fR NUM
+select how genomes are named (default 0)
+0 = use Fasta id
+1 = enumerate beginning with 1
+.TP
+\fB\-rn\fR, \fB\-\-read\-naming\fR NUM
+select how reads are named (default 0)
+0 = use Fasta id
+1 = enumerate beginning with 1
+2 = use the read sequence (only for short reads!)
+.TP
+\fB\-so\fR, \fB\-\-sort\-order\fR NUM
+select how matches are sorted (default 0)
+0 = 1. read number, 2. genome position
+1 = 1. genome position, 2. read number
+.TP
+\fB\-pf\fR, \fB\-\-position\-format\fR NUM
+select begin/end position numbering (default 0)
+0 = gap space
+1 = position space
+.SS "Filtration Options:"
+.TP
+\fB\-s\fR, \fB\-\-shape\fR BITSTRING
+set k\-mer shape (default 11111111111)
+.TP
+\fB\-t\fR, \fB\-\-threshold\fR NUM
+set minimum k\-mer threshold (default 1)
+.TP
+\fB\-oc\fR, \fB\-\-overabundance\-cut\fR NUM
+set k\-mer overabundance cut ratio (default 1)
+.TP
+\fB\-rl\fR, \fB\-\-repeat\-length\fR NUM
+set simple\-repeat length threshold (default 1000)
+.TP
+\fB\-tl\fR, \fB\-\-taboo\-length\fR NUM
+set taboo length (default 1)
+.SS "Verification Options:"
+.TP
+\fB\-mN\fR, \fB\-\-match\-N\fR
+\&'N' matches with all other characters
+.TP
+\fB\-ed\fR, \fB\-\-error\-distr\fR FILE
+write error distribution to FILE
+.SH AUTHOR
+.br
+razers was written by David Weese.
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
Modified: trunk/packages/seqan/trunk/debian/rules
===================================================================
--- trunk/packages/seqan/trunk/debian/rules 2009-09-30 19:23:13 UTC (rev 4099)
+++ trunk/packages/seqan/trunk/debian/rules 2009-09-30 21:00:40 UTC (rev 4100)
@@ -2,6 +2,31 @@
include /usr/share/cdbs/1/rules/debhelper.mk
+build/seqan-apps:: debian/stamp-build-seqan-apps
+debian/stamp-build-seqan-apps:
+ ( cd $(CURDIR)/apps && make )
+ touch $@
+
+install/seqan-apps:: debian/stamp-install-seqan-apps
+debian/stamp-install-seqan-apps:
+ mkdir -p $(CURDIR)/debian/seqan-apps/usr/bin
+ mkdir -p $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps
+ #install binaries
+ cp -p $(CURDIR)/apps/dfi/dfi $(CURDIR)/debian/seqan-apps/usr/bin/
+ cp -p $(CURDIR)/apps/micro_razers/micro_razers $(CURDIR)/debian/seqan-apps/usr/bin/
+ cp -p $(CURDIR)/apps/pair_align/pair_align $(CURDIR)/debian/seqan-apps/usr/bin/
+ cp -p $(CURDIR)/apps/razers/razers $(CURDIR)/debian/seqan-apps/usr/bin/
+ cp -p $(CURDIR)/apps/seqan_tcoffee/seqan_tcoffee $(CURDIR)/debian/seqan-apps/usr/bin/
+ cp -p $(CURDIR)/apps/seqcons/seqcons $(CURDIR)/debian/seqan-apps/usr/bin/
+ cp -p $(CURDIR)/apps/tree_recon/tree_recon $(CURDIR)/debian/seqan-apps/usr/bin/
+ #install readmes
+ cp -p $(CURDIR)/apps/dfi/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.dfi
+ cp -p $(CURDIR)/apps/micro_razers/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.micro_razers
+ cp -p $(CURDIR)/apps/razers/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.razers
+ cp -p $(CURDIR)/apps/seqan_tcoffee/README $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.seqan_tcoffee
+
+ touch $@
+
install/seqan-dev:: debian/stamp-install-seqan-dev
debian/stamp-install-seqan-dev:
mkdir -p $(CURDIR)/debian/seqan-dev/usr/include
@@ -9,7 +34,6 @@
cp -a $(CURDIR)/seqan $(CURDIR)/debian/seqan-dev/usr/include/
cp -a $(CURDIR)/demos $(CURDIR)/debian/seqan-dev/usr/share/doc/seqan-dev
cp -a $(CURDIR)/doc $(CURDIR)/debian/seqan-dev/usr/share/doc/seqan-dev
-
touch $@
get-orig-source:
Added: trunk/packages/seqan/trunk/debian/seqan_tcoffee.1
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan_tcoffee.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/seqan_tcoffee.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,90 @@
+.TH SEQAN_TCOFFEE "1" "September 2009" "Version 1.11 (30. July 2009) Revision: 4637" "User Commands"
+.SH NAME
+seqan_tcoffee \- manual page for Version 1.11 (30. July 2009) Revision: 4637
+.SH SYNOPSIS
+.B seqan_tcoffee
+\fI-s <FASTA sequence file> \fR[\fIOptions\fR]
+.SH DESCRIPTION
+Multiple sequence alignment \- SeqAn::T\-Coffee
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+displays this help message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version information
+.SS "Main Options:"
+.TP
+\fB\-s\fR, \fB\-\-seq\fR <FASTA Sequence File>
+file with sequences
+.TP
+\fB\-a\fR, \fB\-\-alphabet\fR [protein | dna | rna]
+sequence alphabet (default protein)
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <Filename>
+output filename (default out.fasta)
+.TP
+\fB\-f\fR, \fB\-\-format\fR [fasta | msf]
+output format (default fasta)
+.SS "Segment Match Generation Options:"
+.TP
+\fB\-m\fR, \fB\-\-method\fR
+list of match generation methods
+\fR global = Global alignments
+\fR local = Local alignments
+\fR overlap = Overlap alignments
+\fR lcs = Longest common subsequence
+\fR Default: global,local
+\IP No spaces in\-between.
+.TP
+\fB\-bl\fR, \fB\-\-blast\fR <File1>,<File2>,...
+list of BLAST match files
+.TP
+\fB\-mu\fR, \fB\-\-mummer\fR <File1>,<File2>,...
+list of MUMmer match files
+.TP
+\fB\-al\fR, \fB\-\-aln\fR <File1>,<File2>,...
+list of FASTA align files
+.TP
+\fB\-li\fR, \fB\-\-lib\fR <File1>,<File2>,...
+list of T\-Coffee libraries
+.SS "Scoring Options:"
+.TP
+\fB\-g\fR, \fB\-\-gop\fR <Int>
+gap open penalty (default \fB\-13\fR)
+.TP
+\fB\-e\fR, \fB\-\-gex\fR <Int>
+gap extension penalty (default \fB\-1\fR)
+.TP
+\fB\-ma\fR, \fB\-\-matrix\fR <Matrix file>
+score matrix (default Blosum62)
+.TP
+\fB\-ms\fR, \fB\-\-msc\fR <Int>
+match score (default 5)
+.TP
+\fB\-mm\fR, \fB\-\-mmsc\fR <Int>
+mismatch penalty (default \fB\-4\fR)
+.SS "Guide Tree Options:"
+.TP
+\fB\-u\fR, \fB\-\-usetree\fR <Newick guide tree>
+tree filename
+.TP
+\fB\-b\fR, \fB\-\-build\fR [nj, min, max, avg, wavg]
+tree building method (default nj)
+\fR nj = Neighbor\-joining
+\fR min = UPGMA single linkage
+\fR max = UPGMA complete linkage
+\fR avg = UPGMA average linkage
+\fR wavg = UPGMA weighted average linkage
+.IP
+Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair.
+.SS "Alignment Evaluation Options:"
+.TP
+\fB\-i\fR, \fB\-\-infile\fR <FASTA alignment file>
+alignment file
+.SH AUTHOR
+.br
+seqan_tcoffee was written by Tobias Rausch.
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
Added: trunk/packages/seqan/trunk/debian/seqcons.1
===================================================================
--- trunk/packages/seqan/trunk/debian/seqcons.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/seqcons.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,69 @@
+.TH SEQCONS "1" "September 2009" "Version 0.22 (06. August 2009) Revision: 4663" "User Commands"
+.SH NAME
+seqcons \- manual page for Version 0.22 (06. August 2009) Revision: 4663
+.SH SYNOPSIS
+.B seqcons
+\fI-r <FASTA file with reads> \fR[\fIOptions\fR]
+.SH DESCRIPTION
+Multi\-read alignment \- SeqCons
+.IP
+seqcons \fB\-a\fR <AMOS message file> [Options]
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+displays this help message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version information
+.SS "Main Options:"
+.TP
+\fB\-r\fR, \fB\-\-reads\fR <FASTA reads file>
+file with reads
+.TP
+\fB\-a\fR, \fB\-\-afg\fR <AMOS afg file>
+message file
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <Filename>
+output filename (default align.txt)
+.TP
+\fB\-f\fR, \fB\-\-format\fR [seqan | afg]
+output format (default afg)
+.TP
+\fB\-m\fR, \fB\-\-method\fR [realign | msa]
+alignment method (default realign)
+.TP
+\fB\-b\fR, \fB\-\-bandwidth\fR <Int>
+bandwidth (default 8)
+.TP
+\fB\-n\fR, \fB\-\-noalign\fR
+no align, only convert input
+.SS "MSA Method Options:"
+.TP
+\fB\-ma\fR, \fB\-\-matchlength\fR <Int>
+min. overlap length (default 15)
+.TP
+\fB\-qu\fR, \fB\-\-quality\fR <Int>
+min. overlap precent identity (default 80)
+.TP
+\fB\-ov\fR, \fB\-\-overlaps\fR <Int>
+min. number of overlaps per read (default 3)
+.TP
+\fB\-wi\fR, \fB\-\-window\fR <Int>
+window size (default 0)
+/*If this parameter is > 0 then all
+.IP
+overlaps within a given window
+are computed.*/
+.SS "ReAlign Method Options:"
+.TP
+\fB\-in\fR, \fB\-\-include\fR
+include contig sequence
+.TP
+\fB\-rm\fR, \fB\-\-rmethod\fR [nw | gotoh]
+realign method (default gotoh)
+.SH AUTHOR
+.br
+seqcons was written by Tobias Rausch
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
Added: trunk/packages/seqan/trunk/debian/tree_recon.1
===================================================================
--- trunk/packages/seqan/trunk/debian/tree_recon.1 (rev 0)
+++ trunk/packages/seqan/trunk/debian/tree_recon.1 2009-09-30 21:00:40 UTC (rev 4100)
@@ -0,0 +1,43 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36.
+.TH VERSION "1" "September 2009" "Version 1.01 (18. August 2009) Revision: 4692" "User Commands"
+.SH NAME
+Version \- manual page for Version 1.01 (18. August 2009) Revision: 4692
+.SH SYNOPSIS
+.B tree_recon
+\fI-m <Phylip distance matrix> \fR[\fIOptions\fR]
+.SH DESCRIPTION
+Tree reconstrucion \- TreeRecon
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+displays this help message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+print version information
+.SS "Main Options:"
+.TP
+\fB\-m\fR, \fB\-\-matrix\fR <Phylip distance matrix>
+file with distance matrix
+At least 3 species required.
+.TP
+\fB\-b\fR, \fB\-\-build\fR [nj, min, max, avg, wavg]
+tree building method (default nj)
+\fR nj = Neighbor\-joining
+\fR min = UPGMA single linkage
+\fR max = UPGMA complete linkage
+\fR avg = UPGMA average linkage
+\fR wavg = UPGMA weighted average linkage
+.IP
+Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair.
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <Filename>
+output filename (default tree.dot)
+.TP
+\fB\-f\fR, \fB\-\-format\fR [dot | newick]
+output format (default dot)
+.SH AUTHOR
+.br
+tree_recon was written by Tobias Rausch.
+.PP
+This manual page was generated using html2man and polished by
+Soeren Sonnenburg <sonne at debian.org>, for the Debian project
+(but may be used by others).
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