Scroll to navigation

MAUVEALIGNER(1) User Commands MAUVEALIGNER(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>
April 2015 mauvealigner 1.2.0+4713