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Function: Filter out maf files. Output goes to standard out
Usage: mafFilter file(s).maf
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Function: Output protein alignments using maf and genePred
Usage: mafGene dbName mafTable genePredTable species.lst output
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Function: Scan maf and output all species used in it.
Usage: mafSpeciesList in.maf out.lst
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Function: 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.
Usage: mafMeFirst in.maf me.list out.maf
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Function: Extract maf sequences for a region from database
Usage: mafFrag database mafTrack chrom start end strand out.maf