./addCols
./ameme
./autoDtd
./autoSql
./autoXml
./ave
./aveCols
./axtChain
./axtSort
./axtSwap
./axtToMaf
./axtToPsl
./bamToPsl
./bedClip
./bedCommonRegions
./bedCoverage
./bedExtendRanges
./bedGeneParts
./bedGraphPack
./bedGraphToBigWig
./bedIntersect
./bedItemOverlapCount
./bedJoinTabOffset
./bedPileUps
./bedRemoveOverlap
./bedRestrictToPositions
./bedSort
./bedToBigBed
./bedToExons
./bedToGenePred
./bedToPsl
./bedWeedOverlapping
./bigBedInfo
./bigBedNamedItems
./bigBedSummary
./bigBedToBed
./bigMafToMaf
./bigPslToPsl
./bigWigAverageOverBed
./bigWigCat
./bigWigCluster
./bigWigCorrelate
./bigWigInfo
./bigWigMerge
./bigWigSummary
./bigWigToBedGraph
./bigWigToWig
./blastToPsl
./blastXmlToPsl
./blat/blat
./blat/gfClient
./blat/gfServer
./calc
./catDir
./catUncomment
./chainAntiRepeat
./chainBridge
./chainFilter
./chainMergeSort
./chainNet
./chainPreNet
./chainSort
./chainSplit
./chainStitchId
./chainSwap
./chainToAxt
./chainToPsl
./chainToPslBasic
./checkAgpAndFa
./checkCoverageGaps
./checkHgFindSpec
./checkTableCoords
./chopFaLines
./chromGraphFromBin
./chromGraphToBin
./clusterGenes
./colTransform
./countChars
./cpg_lh
./crTreeIndexBed
./crTreeSearchBed
./dbSnoop
./dbTrash
./endsInLf
./estOrient
./expMatrixToBarchartBed
./faAlign
./faCmp
./faCount
./faFilter
./faFilterN
./faFrag
./faNoise
./faOneRecord
./faPolyASizes
./faRandomize
./faRc
./faSize
./faSomeRecords
./faSplit
./faToFastq
./faToTab
./faToTwoBit
./faTrans
./fastqStatsAndSubsample
./fastqToFa
./featureBits
./fetchChromSizes
./findMotif
./gapToLift
./genePredCheck
./genePredFilter
./genePredHisto
./genePredSingleCover
./genePredToBed
./genePredToBigGenePred
./genePredToFakePsl
./genePredToGtf
./genePredToMafFrames
./genePredToProt
./gensub2
./getRna
./getRnaPred
./gff3ToGenePred
./gff3ToPsl
./gmtime
./gtfToGenePred
./headRest
./hgBbiDbLink
./hgFakeAgp
./hgFindSpec
./hgGcPercent
./hgLoadBed
./hgLoadChain
./hgLoadMaf
./hgLoadMafSummary
./hgLoadNet
./hgLoadOut
./hgLoadOutJoined
./hgLoadSqlTab
./hgLoadWiggle
./hgSpeciesRna
./hgTrackDb
./hgWiggle
./hgsql
./hgsqldump
./htmlCheck
./hubCheck
./hubPublicCheck
./ixIxx
./lavToAxt
./lavToPsl
./ldHgGene
./liftOver
./liftOverMerge
./liftUp
./linesToRa
./localtime
./mafAddIRows
./mafAddQRows
./mafCoverage
./mafFetch
./mafFilter
./mafFrag
./mafFrags
./mafGene
./mafMeFirst
./mafOrder
./mafRanges
./mafSpeciesList
./mafSpeciesSubset
./mafSplit
./mafSplitPos
./mafToAxt
./mafToBigMaf
./mafToPsl
./mafToSnpBed
./mafsInRegion
./makeTableList
./maskOutFa
./mktime
./mrnaToGene
./netChainSubset
./netClass
./netFilter
./netSplit
./netSyntenic
./netToAxt
./netToBed
./newProg
./newPythonProg
./nibFrag
./nibSize
./oligoMatch
./overlapSelect
./para
./paraFetch
./paraHub
./paraHubStop
./paraNode
./paraNodeStart
./paraNodeStatus
./paraNodeStop
./paraSync
./paraTestJob
./parasol
./positionalTblCheck
./pslCDnaFilter
./pslCat
./pslCheck
./pslDropOverlap
./pslFilter
./pslHisto
./pslLiftSubrangeBlat
./pslMap
./pslMapPostChain
./pslMrnaCover
./pslPairs
./pslPartition
./pslPosTarget
./pslPretty
./pslRc
./pslRecalcMatch
./pslReps
./pslScore
./pslSelect
./pslSomeRecords
./pslSort
./pslStats
./pslSwap
./pslToBed
./pslToBigPsl
./pslToChain
./pslToPslx
./pslxToFa
./qaToQac
./qacAgpLift
./qacToQa
./qacToWig
./raSqlQuery
./raToLines
./raToTab
./randomLines
./rmFaDups
./rowsToCols
./sizeof
./spacedToTab
./splitFile
./splitFileByColumn
./sqlToXml
./stringify
./subChar
./subColumn
./tailLines
./tdbQuery
./textHistogram
./tickToDate
./toLower
./toUpper
./transMapPslToGenePred
./trfBig
./twoBitDup
./twoBitInfo
./twoBitMask
./twoBitToFa
./vai.pl
./validateFiles
./validateManifest
./webSync
./wigCorrelate
./wigEncode
./wigToBigWig
./wordLine
./xmlCat
./xmlToSql