NAME

       addUnalignedIntervals - part of mauveAligner package
       alignmentProjector - part of mauveAligner package
       backbone_global_to_local - part of mauveAligner package
       bbAnalyze - part of mauveAligner package
       createBackboneMFA - part of mauveAligner package
       getAlignmentWindows - part of mauveAligner package
       getOrthologList - part of mauveAligner package
       makeBadgerMatrix - part of mauveAligner package
       mauveToXMFA - part of mauveAligner package
       mfa2xmfa - part of mauveAligner package
       projectAndStrip - part of mauveAligner package
       randomGeneSample - part of mauveAligner package
       scoreAlignment - part of mauveAligner package
       stripGapColumns - part of mauveAligner package
       stripSubsetLCBs - part of mauveAligner package
       toGrimmFormat - part of mauveAligner package
       toMultiFastA - part of mauveAligner package
       toRawSequence - part of mauveAligner package
       uniqueMerCount - part of mauveAligner package
       uniquifyTrees - part of mauveAligner package
       xmfa2maf - part of mauveAligner package

DESCRIPTION

       These  tools  belong  to the mauveAligner package.  They are not explicitly documented but are printing a
       synopsis line which is repeated here.

       addUnalignedIntervals <input interval file> <output interval file>

       alignmentProjector <input xmfa> <output xmfa> <mfa seq input> <mfa seq output> <list of seqs to  include,
       starting at 0>

       backbone_global_to_local <xmfa file> <backbone file> <output file>

       bbAnalyze  <xmfa  file>  <guide  tree>  <backbone  seqpos file> <backbone col file> <annotated seq index>
       <output file>

              annotated seq index starts at 0.

       createBackboneMFA <input interval file> <output MFA name>

       getAlignmentWindows <XMFA alignment> <window length> <window shift amount> <base output filename>

       getOrthologList getOrthologList <input  xmfa>  <backbone  seq  file>  <reference  genome>  <CDS  ortholog
       filename> <CDS alignment base name>

       makeBadgerMatrix makeBadgerMatrix <input xmfa> <output badger file> <LCB coordinate file>

       mauveToXMFA mauveToXMFA <Mauve Alignment input> <XMFA output>

       mfa2xmfa <MFA alignment input> <XMFA alignment output> [Unaligned FastA output]

       projectAndStrip <input xmfa> <output xmfa> <seq1> <seq2>...<seqN>

              Numeric sequence identifiers start at 0.

       randomGeneSample  <input  xmfa>  <backbone seq file> <sample genome> <number of genes> <output base name>
       [random seed]

       scoreAlignment <correct alignment> <calculated alignment> [evolved sequence file] [slagan]

       stripGapColumns <input XMFA> <output XMFA>

       stripSubsetLCBs <input xmfa> <input  bbcols>  <output  xmfa>  [min  LCB  size]  [min  genomes]  [randomly
       subsample to X kb]

       toGrimmFormat <Mauve Alignment> <genome 1 chr lengths>...<genome N chr lengths>

       toMultiFastA <input interval file> <output base name>

       toRawSequence <input sequence> <output file>

       uniqueMerCount <Sorted Mer List>

       uniquifyTrees <nexus input file> <nexus output file>

              All trees in the input file must have the same number of taxa and the same taxon labels

       xmfa2maf <xmfa input> <maf output>