mauveAligner File List

Here is a list of all files with brief descriptions:
src/addUnalignedIntervals.cpp [code]
src/alignmentProjector.cpp [code]
src/AlignmentTree.cpp [code]
src/AlignmentTree.h [code]
src/backbone_global_to_local.cpp [code]
src/bbAnalyze.cpp [code]
src/bbBreakOnGenes.cpp [code]
src/bbFilter.cpp [code]
src/calculateBackboneCoverage.cpp [code]
src/calculateBackboneCoverage2.cpp [code]
src/calculateCoverage.cpp [code]
src/checkForLGT.cpp [code]
src/coordinateTranslate.cpp [code]
src/countInPlaceInversions.cpp [code]
src/createBackboneMFA.cpp [code]
src/evd.cpp [code]
src/extractBackbone.cpp [code]
src/extractBackbone2.cpp [code]
src/extractBCITrees.cpp [code]
src/extractSubalignments.cpp [code]
src/gappiness.cpp [code]
src/getAlignmentWindows.cpp [code]
src/getOrthologList.cpp [code]
src/joinAlignmentFiles.cpp [code]
src/makeBadgerMatrix.cpp [code]
src/makeMc4Matrix.cpp [code]
src/MatchRecord.h [code]
src/mauveAligner.cpp [code]
src/mauveAligner.h [code]
src/mauveToXMFA.cpp [code]
src/mfa2xmfa.cpp [code]
src/multiEVD.cpp [code]
src/multiToRawSequence.cpp [code]
src/pairCompare.cpp [code]
src/progressiveMauve.cpp [code]
src/projectAndStrip.cpp [code]
src/randomGeneSample.cpp [code]
src/RepeatHashCat.cpp [code]
src/RepeatHashCat.h [code]
src/repeatoire.cpp [code]
src/rootTrees.cpp [code]
src/scoreAlignment.cpp [code]
src/scoreALU.cpp [code]
src/scoreProcrastAlignment.cpp [code]
src/SeedMatchEnumerator.h [code]
src/sortContigs.cpp [code]
src/stripGapColumns.cpp [code]
src/stripSubsetLCBs.cpp [code]
src/toEvoHighwayFormat.cpp [code]
src/toGBKsequence.cpp [code]
src/toGrimmFormat.cpp [code]
src/toMultiFastA.cpp [code]
src/toRawSequence.cpp [code]
src/transposeCoordinates.cpp [code]
src/unalign.cpp [code]
src/UniqueMatchFinder.cpp [code]
src/UniqueMatchFinder.h [code]
src/uniqueMerCount.cpp [code]
src/uniquifyTrees.cpp [code]
src/xmfa2maf.cpp [code]

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