Software Usage Function
mafSplit mafSplit splits.bed outRoot file(s).maf Split multiple alignment files
mafsInRegion mafsInRegion regions.bed out.maf|outDir in.maf(s) Extract MAFs in genomic regions
mafSpeciesSubset mafSpeciesSubset in.maf species.lst out.maf Extract a maf that just has a subset of species.
mafToPsl mafToPsl querySrc targetSrc in.maf out.psl Convert maf to psl format
mafOrder mafOrder mafIn order.lst mafOut Order components within a maf file
mafRanges mafRanges in.maf db out.bed Extract ranges of target (or query) coverage from maf and output as BED 3 (e.g. for processing by featureBits).
genePredToMafFrames genePredToMafFrames [options] targetDb maf mafFrames geneDb1 genePred1 [geneDb2 genePred2...] Create frame annotations for one or more components of a MAF. It is significantly faster to process multiple gene sets in the same"run, as 95% of the CPU time is spent reading the MAF
mafCoverage mafCoverage database mafFile Analyse coverage by maf files - chromosome bychromosome and genome-wide.
mafFrags mafFrags database track in.bed out.maf Collect MAFs from regions specified in a 6 column bed file
mafToAxt mafToAxt in.maf tName qName output Convert from maf to axt format
mafGene mafGene dbName mafTable genePredTable species.lst output Output protein alignments using maf and genePred
mafAddIRows mafAddIRows mafIn twoBitFile mafOut Add 'i' rows to a maf
mafAddQRows mafAddQRows species.lst in.maf out.maf Add quality data to a maf
axtToMaf axtToMaf in.axt tSizes qSizes out.maf Convert from axt to maf format
mafSplitPos mafSplitPos database size(Mbp) out.bed Pick positions to split multiple alignment input files
mafSpeciesList mafSpeciesList in.maf out.lst Scan maf and output all species used in it.
mafFetch mafFetch db table overBed mafOut Get overlapping records from an MAF using an index table
mafFilter mafFilter file(s).maf Filter out maf files. Output goes to standard out
mafMeFirst mafMeFirst in.maf me.list out.maf Move component to top if it is one of the named ones.Useful in conjunction with mafFrags when you don't want the one withthe gene name to be in the middle.
mafFrag mafFrag database mafTrack chrom start end strand out.maf Extract maf sequences for a region from database