alignmentProjector(1)
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>
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