Category

Multiple sequence alignments / Conservation


Usage

axtToMaf in.axt tSizes qSizes out.maf


Manual

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

Where tSizes and qSizes is a file that contains
the sizes of the target and query sequences.
Very often this with be a chrom.sizes file
Options:
-qPrefix=XX. - add XX. to start of query sequence name in maf
-tPrefex=YY. - add YY. to start of target sequence name in maf
-tSplit Create a separate maf file for each target sequence.
In this case output is a dir rather than a file
In this case in.maf must be sorted by target.
-score - recalculate score
-scoreZero- recalculate score if zero


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