Multiple sequence alignments / Conservation

mafSplit
Function: Split multiple alignment files
Usage: mafSplit splits.bed outRoot file(s).maf
Supported input format: MAF
mafsInRegion
Function: Extract MAFs in genomic regions
Usage: mafsInRegion regions.bed out.maf|outDir in.maf(s)
Supported input format: MAF
mafSpeciesSubset
Function: Extract a maf that just has a subset of species.
Usage: mafSpeciesSubset in.maf species.lst out.maf
mafToPsl
Function: Convert maf to psl format
Usage: mafToPsl querySrc targetSrc in.maf out.psl
mafFrags
Function: Collect MAFs from regions specified in a 6 column bed file
Usage: mafFrags database track in.bed out.maf
mafToAxt
Function: Convert from maf to axt format
Usage: mafToAxt in.maf tName qName output
mafOrder
Function: Order components within a maf file
Usage: mafOrder mafIn order.lst mafOut
axtToMaf
Function: Convert from axt to maf format
Usage: axtToMaf in.axt tSizes qSizes out.maf
mafRanges
Function: Extract ranges of target (or query) coverage from maf and output as BED 3 (e.g. for processing by featureBits).
Usage: mafRanges in.maf db out.bed
mafCoverage
Function: Analyse coverage by maf files - chromosome bychromosome and genome-wide.
Usage: mafCoverage database mafFile
mafFetch
Function: Get overlapping records from an MAF using an index table
Usage: mafFetch db table overBed mafOut
mafSplitPos
Function: Pick positions to split multiple alignment input files
Usage: mafSplitPos database size(Mbp) out.bed
genePredToMafFrames
Function: 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
Usage: genePredToMafFrames [options] targetDb maf mafFrames geneDb1 genePred1 [geneDb2 genePred2...]
mafAddIRows
Function: Add 'i' rows to a maf
Usage: mafAddIRows mafIn twoBitFile mafOut
mafFilter
Function: Filter out maf files. Output goes to standard out
Usage: mafFilter file(s).maf