.\" 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