Category

Multiple sequence alignments / Conservation


Usage

mafFilter file(s).maf


Manual

This tool is part of UCSC Genome Browser's utilities.

options:
-tolerate - Just ignore bad input rather than aborting.
-minCol=N - Filter out blocks with fewer than N columns (default 1)
-minRow=N - Filter out blocks with fewer than N rows (default 2)
-maxRow=N - Filter out blocks with >= N rows (default 100)
-factor - Filter out scores below -minFactor * (ncol**2) * nrow
-minFactor=N - Factor to use with -minFactor (default 5)
-minScore=N - Minimum allowed score (alternative to -minFactor)
-reject=filename - Save rejected blocks in filename
-needComp=species - all alignments must have species as one of the component
-overlap - Reject overlapping blocks in reference (assumes ordered blocks)
-componentFilter=filename - Filter out blocks without a component listed in filename
-speciesFilter=filename - Filter out blocks without a species listed in filename


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