addUnalignedIntervals - 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<inputintervalfile><outputintervalfile>alignmentProjector<inputxmfa><outputxmfa><mfaseqinput><mfaseqoutput><listofseqstoinclude,startingat0>backbone_global_to_local<xmfafile><backbonefile><outputfile>bbAnalyze<xmfafile><guidetree><backboneseqposfile><backbonecolfile><annotatedseqindex><outputfile>

              annotated seq index starts at 0.

       createBackboneMFA<inputintervalfile><outputMFAname>getAlignmentWindows<XMFAalignment><windowlength><windowshiftamount><baseoutputfilename>getOrthologListgetOrthologList<inputxmfa><backboneseqfile><referencegenome><CDSorthologfilename><CDSalignmentbasename>makeBadgerMatrixmakeBadgerMatrix<inputxmfa><outputbadgerfile><LCBcoordinatefile>mauveToXMFAmauveToXMFA<MauveAlignmentinput><XMFAoutput>mfa2xmfa<MFAalignmentinput><XMFAalignmentoutput>[UnalignedFastAoutput]projectAndStrip<inputxmfa><outputxmfa><seq1><seq2>...<seqN>

              Numeric sequence identifiers start at 0.

       randomGeneSample<inputxmfa><backboneseqfile><samplegenome><numberofgenes><outputbasename>[randomseed]scoreAlignment<correctalignment><calculatedalignment>[evolvedsequencefile][slagan]stripGapColumns<inputXMFA><outputXMFA>stripSubsetLCBs<inputxmfa><inputbbcols><outputxmfa>[minLCBsize][mingenomes][randomlysubsampletoXkb]toGrimmFormat<MauveAlignment><genome1chrlengths>...<genomeNchrlengths>toMultiFastA<inputintervalfile><outputbasename>toRawSequence<inputsequence><outputfile>uniqueMerCount<SortedMerList>uniquifyTrees<nexusinputfile><nexusoutputfile>

              All trees in the input file must have the same number of taxa and the same taxon labels

       xmfa2maf<xmfainput><mafoutput>

mauvealigner 1.2.0+4713                            April 2015                                    MAUVEALIGNER(1)

       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