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getAlignmentWindows - Online in the Cloud

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This is the command getAlignmentWindows that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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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