||mafSplit splits.bed outRoot file(s).maf
||Split multiple alignment files
||mafsInRegion regions.bed out.maf|outDir in.maf(s)
||Extract MAFs in genomic regions
||mafSpeciesSubset in.maf species.lst out.maf
||Extract a maf that just has a subset of species.
||mafToPsl querySrc targetSrc in.maf out.psl
||Convert maf to psl format
||mafOrder mafIn order.lst mafOut
||Order components within a maf file
||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 [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 database mafFile
||Analyse coverage by maf files - chromosome bychromosome and genome-wide.
||mafFrags database track in.bed out.maf
||Collect MAFs from regions specified in a 6 column bed file
||mafToAxt in.maf tName qName output
||Convert from maf to axt format
||mafGene dbName mafTable genePredTable species.lst output
||Output protein alignments using maf and genePred
||mafAddQRows species.lst in.maf out.maf
||Add quality data to a maf
||mafAddIRows mafIn twoBitFile mafOut
||Add 'i' rows to a maf
||axtToMaf in.axt tSizes qSizes out.maf
||Convert from axt to maf format
||mafSplitPos database size(Mbp) out.bed
||Pick positions to split multiple alignment input files
||mafSpeciesList in.maf out.lst
||Scan maf and output all species used in it.
||mafFetch db table overBed mafOut
||Get overlapping records from an MAF using an index table
||Filter out maf files. Output goes to standard out
||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 database mafTrack chrom start end strand out.maf
||Extract maf sequences for a region from database