[med-svn] [mauvealigner] 07/08: Add manpages basically created using help2man

Andreas Tille tille at debian.org
Mon Apr 20 16:56:01 UTC 2015 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository mauvealigner.

commit 29c505a6d8b2939288279a8f384662f3b3d22657
Author: Andreas Tille <tille at debian.org>
Date:   Mon Apr 20 17:23:44 2015 +0200

    Add manpages basically created using help2man
---
 debian/links                       |  20 +++++++
 debian/man/addUnalignedIntervals.1 |  95 +++++++++++++++++++++++++++++++
 debian/man/bbFilter.1              |  20 +++++++
 debian/man/coordinateTranslate.1   |  10 ++++
 debian/man/extractBCITrees.1       |  14 +++++
 debian/man/mauveAligner.1          |  77 +++++++++++++++++++++++++
 debian/man/progressiveMauve.1      | 108 +++++++++++++++++++++++++++++++++++
 debian/man/repeatoire.1            | 114 +++++++++++++++++++++++++++++++++++++
 debian/manpages                    |   1 +
 9 files changed, 459 insertions(+)

diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..6ff54b8
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,20 @@
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/alignmentProjector.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/backbone_global_to_local.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/bbAnalyze.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/createBackboneMFA.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/getAlignmentWindows.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/getOrthologList.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/makeBadgerMatrix.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/mauveToXMFA.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/mfa2xmfa.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/projectAndStrip.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/randomGeneSample.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/scoreAlignment.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/stripGapColumns.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/stripSubsetLCBs.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/toGrimmFormat.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/toMultiFastA.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/toRawSequence.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/uniqueMerCount.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/uniquifyTrees.1.gz
+/usr/share/man/man1/addUnalignedIntervals.1.gz /usr/share/man/man1/xmfa2maf.1.gz
diff --git a/debian/man/addUnalignedIntervals.1 b/debian/man/addUnalignedIntervals.1
new file mode 100644
index 0000000..86dfe8e
--- /dev/null
+++ b/debian/man/addUnalignedIntervals.1
@@ -0,0 +1,95 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH MAUVEALIGNER "1" "April 2015" "mauvealigner 1.2.0+4713" "User Commands"
+.SH NAME
+addUnalignedIntervals - part of mauveAligner package
+.br
+alignmentProjector - part of mauveAligner package
+.br
+backbone_global_to_local - part of mauveAligner package
+.br
+bbAnalyze - part of mauveAligner package
+.br
+createBackboneMFA - part of mauveAligner package
+.br
+getAlignmentWindows - part of mauveAligner package
+.br
+getOrthologList - part of mauveAligner package
+.br
+makeBadgerMatrix - part of mauveAligner package
+.br
+mauveToXMFA - part of mauveAligner package
+.br
+mfa2xmfa - part of mauveAligner package
+.br
+projectAndStrip - part of mauveAligner package
+.br
+randomGeneSample - part of mauveAligner package
+.br
+scoreAlignment - part of mauveAligner package
+.br
+stripGapColumns - part of mauveAligner package
+.br
+stripSubsetLCBs - part of mauveAligner package
+.br
+toGrimmFormat - part of mauveAligner package
+.br
+toMultiFastA - part of mauveAligner package
+.br
+toRawSequence - part of mauveAligner package
+.br
+uniqueMerCount - part of mauveAligner package
+.br
+uniquifyTrees - part of mauveAligner package
+.br
+xmfa2maf - part of mauveAligner package
+.SH DESCRIPTION
+These tools belong to the mauveAligner package.  They are not explicitly
+documented but are printing a synopsis line which is repeated here.
+.PP
+\fBaddUnalignedIntervals\fR \fI<input interval file> <output interval file>\fR
+.PP
+\fBalignmentProjector\fR \fI<input xmfa> <output xmfa> <mfa seq input> <mfa seq output> <list of seqs to include, starting at 0>\fR
+.PP
+\fBbackbone_global_to_local\fR \fI<xmfa file> <backbone file> <output file>\fR
+.PP
+\fBbbAnalyze\fR \fI<xmfa file> <guide tree> <backbone seqpos file> <backbone col file> <annotated seq index> <output file>\fR
+.IP
+annotated seq index starts at 0.
+.PP
+\fBcreateBackboneMFA\fR \fI<input interval file> <output MFA name>\fR
+.PP
+\fBgetAlignmentWindows\fR \fI<XMFA alignment> <window length> <window shift amount> <base output filename>\fR
+.PP
+\fBgetOrthologList\fR \fIgetOrthologList <input xmfa> <backbone seq file> <reference genome> <CDS ortholog filename> <CDS alignment base name>\fR
+.PP
+\fBmakeBadgerMatrix\fR \fImakeBadgerMatrix <input xmfa> <output badger file> <LCB coordinate file>\fR
+.PP
+\fBmauveToXMFA\fR \fImauveToXMFA <Mauve Alignment input> <XMFA output>\fR
+.PP
+\fBmfa2xmfa\fR \fI<MFA alignment input> <XMFA alignment output> [Unaligned FastA output]\fR
+.PP
+\fBprojectAndStrip\fR \fI<input xmfa> <output xmfa> <seq1> <seq2>...<seqN>\fR
+.IP
+Numeric sequence identifiers start at 0.
+.PP
+\fBrandomGeneSample\fR \fI<input xmfa> <backbone seq file> <sample genome> <number of genes> <output base name> [random seed]\fR
+.PP
+\fBscoreAlignment\fR \fI<correct alignment> <calculated alignment> [evolved sequence file] [slagan]\fR
+.PP
+\fBstripGapColumns\fR \fI<input XMFA> <output XMFA>\fR
+.PP
+\fBstripSubsetLCBs\fR \fI<input xmfa> <input bbcols> <output xmfa> [min LCB size] [min genomes] [randomly subsample to X kb]\fR
+.PP
+\fBtoGrimmFormat\fR \fI<Mauve Alignment> <genome 1 chr lengths>...<genome N chr lengths>\fR
+.PP
+\fBtoMultiFastA\fR \fI<input interval file> <output base name>\fR
+.PP
+\fBtoRawSequence\fR \fI<input sequence> <output file>\fR
+.PP
+\fBuniqueMerCount\fR \fI<Sorted Mer List>\fR
+.PP
+\fBuniquifyTrees\fR \fI<nexus input file> <nexus output file>\fR
+.IP
+All trees in the input file must have the same number of taxa and the same taxon labels
+.PP
+\fBxmfa2maf\fR \fI<xmfa input> <maf output>\fR
diff --git a/debian/man/bbFilter.1 b/debian/man/bbFilter.1
new file mode 100644
index 0000000..2ce2b59
--- /dev/null
+++ b/debian/man/bbFilter.1
@@ -0,0 +1,20 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH BBFILTER "1" "April 2015" "bbFilter 1.2.0+4713" "User Commands"
+.SH NAME
+bbFilter \- this is a part of mauveAligner package
+.SH DESCRIPTION
+\fBbbFilter\fR \fI<backbone file> <independent dist> <output file> <beast|gp> [<seq1> <seq2>...<seqN>]\fR
+.br
+seq index starts at 0.
+.SH EXAMPLES
+Example:
+.IP
+\fBbbFilter\fR my_alignment.backbone 50 my_feats.bin gp
+.PP
+the above command extracts binary features from "my_alignment.backbone" which are separated by a minimum of 50nt sequence conserved among all taxa in the alignment.  The output is written to my_feats.bin in genoplast format
+.PP
+Example 2:
+.IP
+\fBbbFilter\fR aln.backbone 100 feats.xml beast 0 1 2 5 6
+.PP
+the above command extracts binary features from "aln.backbone" which are separated by a minimum of 100nt sequence conserved among genomes 0,1,2,5, and 6 from the alignment.  The output is written to feats.xml in beast format
diff --git a/debian/man/coordinateTranslate.1 b/debian/man/coordinateTranslate.1
new file mode 100644
index 0000000..f7967ce
--- /dev/null
+++ b/debian/man/coordinateTranslate.1
@@ -0,0 +1,10 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH COORDINATETRANSLATE "1" "April 2015" "coordinateTranslate 1.2.0+4713" "User Commands"
+.SH NAME
+coordinateTranslate \- part of mauveAligner package
+.SH SYNOPSIS
+.B coordinateTranslate
+\fI\,<XMFA alignment> <alignment coordinate file>\/\fR
+.SH DESCRIPTION
+Alignment coordinate file should be structured into 2 tab\-delimited columns: <block ID> <column>
+Output will be the nearest aligned position for each genome in the block, with 0 entries for genomes undefined in the block
diff --git a/debian/man/extractBCITrees.1 b/debian/man/extractBCITrees.1
new file mode 100644
index 0000000..d83ea56
--- /dev/null
+++ b/debian/man/extractBCITrees.1
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH EXTRACTBCITREES "1" "April 2015" "extractBCITrees 1.2.0+4713" "User Commands"
+.SH NAME
+extractBCITrees \- part of mauveAligner package reads all trees and their posterior from a set of MrBayes .trprobs files
+.SH SYNOPSIS
+.B extractBCITrees
+\fI\,<random seed> <BCI threshold> <max output trees> <MrBayes .trprobs input file 1 \/\fR.. \fI\,N> <nexus output file>\/\fR
+.SH DESCRIPTION
+This program reads all trees and their posterior from a set of MrBayes .trprobs files
+and sums and normalizes posteriors for each topology.  All trees that meet a Bayes Credible
+Interval threshold will be saved, up to some maximum number of trees.
+<BCI Threshold> A number between 0 and 1 giving the BCI threshold.  0.9 is a good choice.
+<max output trees>      Limit the output to this many trees.
+All trees in the input file must have the same number of taxa and the same taxon labels
diff --git a/debian/man/mauveAligner.1 b/debian/man/mauveAligner.1
new file mode 100644
index 0000000..49b36de
--- /dev/null
+++ b/debian/man/mauveAligner.1
@@ -0,0 +1,77 @@
+.TH MAUVEALIGNER "1" "April 2015" "mauveAligner 1.2.0+4713" "User Commands"
+.SH NAME
+mauveAligner \- efficiently constructing multiple genome alignments
+.SH SYNOPSIS
+mauveAligner [options] <seq1 filename> <sml1 filename> ...  <seqN filename> <smlN filename>
+.SH DESCRIPTION
+The mauveAligner and progressiveMauve alignment algorithms have been
+implemented as command-line programs included with the downloadable Mauve
+software.  When run from the command-line, these programs provide options
+not yet available in the graphical interface.
+.SH OPTIONS
+.TP
+\fB\-\-output=\fR<file> Output file name.
+Prints to screen by default
+.TP
+\fB\-\-mums\fR Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)
+.TP
+\fB\-\-no\-recursion\fR Don't perform recursive anchor identification (implies \fB\-\-no\-gapped\-alignment\fR)
+.TP
+\fB\-\-no\-lcb\-extension\fR If determining LCBs, don't attempt to extend the LCBs
+.TP
+\fB\-\-seed\-size=\fR<number> Initial seed match size, default is log_2( average seq. length )
+.TP
+\fB\-\-max\-extension\-iterations=\fR<number> Limit LCB extensions to this number of attempts, default is 4
+.TP
+\fB\-\-eliminate\-inclusions\fR Eliminate linked inclusions in subset matches.
+.TP
+\fB\-\-weight=\fR<number> Minimum LCB weight in base pairs per sequence
+.TP
+\fB\-\-match\-input=\fR<file> Use specified match file instead of searching for matches
+.TP
+\fB\-\-lcb\-match\-input\fR  Indicates that the match input file contains matches that have been clustered into LCBs
+.TP
+\fB\-\-lcb\-input=\fR<file> Use specified lcb file instead of constructing LCBs (skips LCB generation)
+.TP
+\fB\-\-scratch\-path=\fR<path>  For large genomes, use a directory for storage of temporary data.  Should be given two or more times to with different paths.
+.TP
+\fB\-\-id\-matrix=\fR<file> Generate LCB stats and write them to the specified file
+.TP
+\fB\-\-island\-size=\fR<number> Find islands larger than the given number
+.TP
+\fB\-\-island\-output=\fR<file> Output islands the given file (requires \fB\-\-island\-size\fR)
+.TP
+\fB\-\-backbone\-size=\fR<number> Find stretches of backbone longer than the given number of b.p.
+.TP
+\fB\-\-max\-backbone\-gap=\fR<number> Allow backbone to be interrupted by gaps up to this length in b.p.
+.TP
+\fB\-\-backbone\-output=\fR<file> Output islands the given file (requires \fB\-\-island\-size\fR)
+.TP
+\fB\-\-coverage\-output=\fR<file> Output a coverage list to the specified file (\- for stdout)
+.TP
+\fB\-\-repeats\fR Generates a repeat map.  Only one sequence can be specified
+.TP
+\fB\-\-output\-guide\-tree=\fR<file> Write out a guide tree to the designated file
+.TP
+\fB\-\-collinear\fR Assume that input sequences are collinear\-\-they have no rearrangements
+.SS "Gapped alignment controls:"
+.TP
+\fB\-\-no\-gapped\-alignment\fR Don't perform a gapped alignment
+.TP
+\fB\-\-max\-gapped\-aligner\-length=\fR<number> Maximum number of base pairs to attempt aligning with the gapped aligner
+.TP
+\fB\-\-min\-recursive\-gap\-length=\fR<number> Minimum size of gaps that Mauve will perform recursive MUM anchoring on (Default is 200)
+.SS "Signed permutation matrix options:"
+.TP
+\fB\-\-permutation\-matrix\-output=\fR<file> Write out the LCBs as a signed permutation matrix to the given file
+.TP
+\fB\-\-permutation\-matrix\-min\-weight=\fR<number> A permutation matrix will be written for every set of LCBs with weight between this value and the value of \fB\-\-weight\fR
+.SS "Alignment output options:"
+.TP
+\fB\-\-alignment\-output\-dir=\fR<directory> Outputs a set of alignment files (one per LCB) to a given directory
+.TP
+\fB\-\-alignment\-output\-format=\fR<directory> Selects the output format for \fB\-\-alignment\-output\-dir\fR
+.TP
+\fB\-\-output\-alignment=\fR<file> Write out an XMFA format alignment to the designated file
+.PP
+Supported alignment output formats are: phylip, clustal, msf, nexus, mega, codon
diff --git a/debian/man/progressiveMauve.1 b/debian/man/progressiveMauve.1
new file mode 100644
index 0000000..ed92c82
--- /dev/null
+++ b/debian/man/progressiveMauve.1
@@ -0,0 +1,108 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH PROGRESSIVEMAUVE "1" "April 2015" "progressiveMauve 1.2.0+4713" "User Commands"
+.SH NAME
+progressiveMauve \- efficiently constructing multiple genome alignments
+.SH DESCRIPTION
+progressiveMauve usage:
+.PP
+When each genome resides in a separate file:
+progressiveMauve [options] <seq1 filename> ... <seqN filename>
+.PP
+When all genomes are in a single file:
+progressiveMauve [options] <seq filename>
+.SH OPTIONS
+.HP
+\fB\-\-island\-gap\-size=\fR<number> Alignment gaps above this size in nucleotides are considered to be islands [20]
+.HP
+\fB\-\-profile=\fR<file> (Not yet implemented) Read an existing sequence alignment in XMFA format and align it to other sequences or alignments
+.HP
+\fB\-\-apply\-backbone=\fR<file> Read an existing sequence alignment in XMFA format and apply backbone statistics to it
+.HP
+\fB\-\-disable\-backbone\fR Disable backbone detection
+.HP
+\fB\-\-mums\fR Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)
+.HP
+\fB\-\-seed\-weight=\fR<number> Use the specified seed weight for calculating initial anchors
+.TP
+\fB\-\-output=\fR<file> Output file name.
+Prints to screen by default
+.HP
+\fB\-\-backbone\-output=\fR<file> Backbone output file name (optional).
+.HP
+\fB\-\-match\-input=\fR<file> Use specified match file instead of searching for matches
+.HP
+\fB\-\-input\-id\-matrix=\fR<file> An identity matrix describing similarity among all pairs of input sequences/alignments
+.HP
+\fB\-\-max\-gapped\-aligner\-length=\fR<number> Maximum number of base pairs to attempt aligning with the gapped aligner
+.HP
+\fB\-\-input\-guide\-tree=\fR<file> A phylogenetic guide tree in NEWICK format that describes the order in which sequences will be aligned
+.HP
+\fB\-\-output\-guide\-tree=\fR<file> Write out the guide tree used for alignment to a file
+.HP
+\fB\-\-version\fR Display software version information
+.HP
+\fB\-\-debug\fR Run in debug mode (perform internal consistency checks\-\-very slow)
+.TP
+\fB\-\-scratch\-path\-1=\fR<path> Designate a path that can be used for temporary data storage.
+Two or more paths should be specified.
+.TP
+\fB\-\-scratch\-path\-2=\fR<path> Designate a path that can be used for temporary data storage.
+Two or more paths should be specified.
+.HP
+\fB\-\-collinear\fR Assume that input sequences are collinear\-\-they have no rearrangements
+.TP
+\fB\-\-scoring\-scheme=\fR<ancestral|sp_ancestral|sp> Selects the anchoring score function.
+Default is extant sum\-of\-pairs (sp).
+.HP
+\fB\-\-no\-weight\-scaling\fR Don't scale LCB weights by conservation distance and breakpoint distance
+.TP
+\fB\-\-max\-breakpoint\-distance\-scale=\fR<number [0,1]> Set the maximum weight scaling by breakpoint distance.
+Defaults to 0.5
+.TP
+\fB\-\-conservation\-distance\-scale=\fR<number [0,1]> Scale conservation distances by this amount.
+Defaults to 0.5
+.TP
+\fB\-\-muscle\-args=\fR<arguments in quotes> Additional command\-line options for MUSCLE.
+Any quotes should be escaped with a backslash
+.HP
+\fB\-\-skip\-refinement\fR Do not perform iterative refinement
+.HP
+\fB\-\-skip\-gapped\-alignment\fR Do not perform gapped alignment
+.HP
+\fB\-\-bp\-dist\-estimate\-min\-score=\fR<number> Minimum LCB score for estimating pairwise breakpoint distance
+.HP
+\fB\-\-mem\-clean\fR Set this to true when debugging memory allocations
+.HP
+\fB\-\-gap\-open=\fR<number> Gap open penalty
+.TP
+\fB\-\-repeat\-penalty=\fR<negative|zero> Sets whether the repeat scores go negative or go to zero for highly repetitive sequences.
+Default is negative.
+.HP
+\fB\-\-gap\-extend=\fR<number> Gap extend penalty
+.HP
+\fB\-\-substitution\-matrix=\fR<file> Nucleotide substitution matrix in NCBI format
+.HP
+\fB\-\-weight=\fR<number> Minimum pairwise LCB score
+.HP
+\fB\-\-min\-scaled\-penalty=\fR<number> Minimum breakpoint penalty after scaling the penalty by expected divergence
+.HP
+\fB\-\-hmm\-p\-go\-homologous=\fR<number> Probability of transitioning from the unrelated to the homologous state [0.00001]
+.HP
+\fB\-\-hmm\-p\-go\-unrelated=\fR<number> Probability of transitioning from the homologous to the unrelated state [0.000000001]
+.HP
+\fB\-\-hmm\-identity=\fR<number> Expected level of sequence identity among pairs of sequences, ranging between 0 and 1 [0.7]
+.HP
+\fB\-\-seed\-family\fR Use a family of spaced seeds to improve sensitivity
+.HP
+\fB\-\-solid\-seeds\fR Use solid seeds. Do not permit substitutions in anchor matches.
+.HP
+\fB\-\-coding\-seeds\fR Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy.
+.HP
+\fB\-\-disable\-cache\fR Disable recursive anchor search cacheing to workaround a crash bug
+.HP
+\fB\-\-no\-recursion\fR Disable recursive anchor search
+.SH EXAMPLES
+progressiveMauve \-\-output=my_seqs.xmfa my_genome1.gbk my_genome2.gbk my_genome3.fasta
+.PP
+If genomes are in a single file and have no rearrangement:
+progressiveMauve \-\-collinear \-\-output=my_seqs.xmfa my_genomes.fasta
diff --git a/debian/man/repeatoire.1 b/debian/man/repeatoire.1
new file mode 100644
index 0000000..4262837
--- /dev/null
+++ b/debian/man/repeatoire.1
@@ -0,0 +1,114 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH REPEATOIRE "1" "April 2015" "repeatoire 1.2.0+4713" "User Commands"
+.SH NAME
+repeatoire \- part of mauveAligner package
+.SH DESCRIPTION
+.SS "Allowed options:"
+.TP
+\fB\-\-allow\-redundant\fR arg (=1)
+allow redundant alignments?
+.TP
+\fB\-\-chain\fR arg (=1)
+chain seeds?
+.TP
+\fB\-\-extend\fR arg (=1)
+perform gapped extension on chains?
+.TP
+\fB\-\-window\fR arg (=\-1)
+size of window to use during gapped
+extension
+.TP
+\fB\-\-gapopen\fR arg (=0)
+gap open penalty
+.TP
+\fB\-\-gapextend\fR arg (=0)
+gap extension penalty
+.TP
+\fB\-\-h\fR arg (=0.00800000038)
+Transition to Homologous
+.TP
+\fB\-\-help\fR
+get help message
+.TP
+\fB\-\-highest\fR arg (=procrast.highest) file containing highest scoring alignment
+for each multiplicity
+.TP
+\fB\-\-l\fR arg (=1)
+minimum repeat length
+.TP
+\fB\-\-large\-repeats\fR arg (=0)
+optimize for large repeats
+.TP
+\fB\-\-load\-sml\fR arg (=0)
+try to load existing SML file?
+.TP
+\fB\-\-onlydirect\fR arg (=0)
+only process seed matches on same strand?
+.TP
+\fB\-\-onlyextended\fR arg (=0)
+only output extended matches?
+.TP
+\fB\-\-output\fR arg
+procrastAligner output
+.TP
+\fB\-\-percentid\fR arg (=0)
+min repeat family % id
+.TP
+\fB\-\-novel\-subsets\fR arg (=0)
+find novel subset matches?
+.TP
+\fB\-\-novel\-matches\fR arg (=1)
+use novel matches found during gapped
+extension?
+.TP
+\fB\-\-rmax\fR arg (=500)
+maximum repeat multiplicity (max copy
+number)
+.TP
+\fB\-\-rmin\fR arg (=2)
+minimum repeat multiplicity (min copy
+number)
+.TP
+\fB\-\-seeds\fR arg
+seed output file
+.TP
+\fB\-\-sequence\fR arg
+FastA sequence file
+.TP
+\fB\-\-small\-repeats\fR arg (=0)
+optimize for small repeats
+.TP
+\fB\-\-score\-out\fR arg
+output with corresponding score and
+alignment info
+.TP
+\fB\-\-solid\fR arg (=0)
+use solid/exact seeds?
+.TP
+\fB\-\-sp\fR arg (=0)
+minimum Sum\-of\-Pairs alignment score
+.TP
+\fB\-\-tandem\fR arg (=1)
+allow tandem repeats?
+.TP
+\fB\-\-two\-hits\fR arg (=0)
+require two hits within w to trigger gapped
+extension?
+.TP
+\fB\-\-u\fR arg (=0.00100000005)
+Transition to Unrelated
+.TP
+\fB\-\-unalign\fR arg (=1)
+unalign non\-homologous sequence?
+.TP
+\fB\-\-w\fR arg (=0)
+max gap width
+.TP
+\fB\-\-xmfa\fR arg
+XMFA format output
+.TP
+\fB\-\-xml\fR arg
+XML format output
+.TP
+\fB\-\-z\fR arg (=0)
+seed weight
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/man/*.1

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