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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


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

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

xmfa2maf <xmfa input> <maf output>

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