[med-svn] [proteinortho] 01/02: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
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commit 7c5eea99fe3cd9a0dd7b94dca6c7b070082b6985
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 12 19:19:56 2015 +0100

    Add manpage
---
 debian/manpages        |   1 +
 debian/proteinortho5.1 | 102 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 103 insertions(+)

diff --git a/debian/manpages b/debian/manpages
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index 0000000..0f65186
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+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/proteinortho5.1 b/debian/proteinortho5.1
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+.TH PROTEINORTHO5 "1" "November 2015" "proteinortho5 5.11" "User Commands"
+.SH NAME
+proteinortho5 \- orthology detection tool
+.SH SYNOPSIS
+.B proteinortho5
+[\fI\,OPTIONS\/\fR] \fI\,FASTA1 FASTA2 \/\fR[\fI\,FASTA\/\fR...]
+.SH DESCRIPTION
+Proteinortho is a stand-alone tool that is geared towards large datasets
+and makes use of distributed computing techniques when run on multi-core
+hardware. It implements an extended version of the reciprocal best
+alignment heuristic. Proteinortho was applied to compute orthologous
+proteins in the complete set of all 717 eubacterial genomes available at
+NCBI at the beginning of 2009. Authors succeeded identifying thirty
+proteins present in 99% of all bacterial proteomes.
+.SH OPTIONS
+.TP
+\fB\-e=\fR
+E\-value for blast [default: 1e\-05]
+.TP
+\fB\-p=\fR
+blast program {blastn|blastp|blastn+|blastp+}
+[default: blastp+]
+.TP
+\fB\-project=\fR
+prefix for all result file names [default: myproject]
+.TP
+\fB\-synteny\fR
+activate PoFF extension to separate similar sequences
+by contextual adjacencies (requires .gff for each .fasta)
+.TP
+\fB\-dups=\fR
+PoFF: number of reiterations for adjacencies heuristic,
+to determine duplicated regions (default: 0)
+.TP
+\fB\-cs=\fR
+PoFF: Size of a maximum common substring (MCS) for
+adjacency matches (default: 3)
+.TP
+\fB\-alpha=\fR
+PoFF: weight of adjacencies vs. sequence similarity
+(default: 0.5)
+.TP
+\fB\-desc\fR
+write description files (for NCBI FASTA input only)
+.TP
+\fB\-keep\fR
+stores temporary blast results for reuse
+.TP
+\fB\-force\fR
+forces recalculation of blast results in any case
+.TP
+\fB\-cpus=\fR
+number of processors to use [default: auto]
+.TP
+\fB\-selfblast\fR
+apply selfblast, detects paralogs without orthologs
+.TP
+\fB\-singles\fR
+report singleton genes without any hit
+.TP
+\fB\-identity=\fR
+min. percent identity of best blast hits [default: 25]
+.TP
+\fB\-cov=\fR
+min. coverage of best blast alignments in % [default: 50]
+.TP
+\fB\-conn=\fR
+min. algebraic connectivity [default: 0.1]
+.TP
+\fB\-sim=\fR
+min. similarity for additional hits (0..1) [default: 0.95]
+.TP
+\fB\-step=\fR
+1 \-> generate indices
+2 \-> run blast (and ff\-adj, if \fB\-synteny\fR is set)
+3 \-> clustering
+0 \-> all (default)
+.TP
+\fB\-blastpath=\fR
+path to your local blast (if not installed globally)
+.TP
+\fB\-verbose\fR
+keeps you informed about the progress
+.TP
+\fB\-clean\fR
+remove all unnecessary files after processing
+.TP
+\fB\-graph\fR
+generate .graph files (pairwise orthology relations)
+.TP
+\fB\-debug\fR
+gives detailed information for bug tracking
+.PP
+More specific blast parameters can be defined by
+.TP
+\fB\-blastParameters=\fR'[parameters]' (e.g. \fB\-blastParameters=\fR'\-seg no')
+.PP
+In case jobs should be distributed onto several machines, use
+.TP
+\fB\-startat=\fR    File number to start with (default: 0)
+.TP
+\fB\-stopat=\fR     File number to end with (default: \fB\-1\fR)

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