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 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>