NAME

       maf2anchors -- Converts maf files into Murasaki anchor sets

SYNOPSIS

       maf2anchors <file.maf>

OPTIONS

       --prefix=<S>
           use <S> as a prefix for output file names (otherwise uses <file.maf>)

       --rifts=<I>
           allow up to <I> rifts.

       --fakeseqs
           generate fake sequence length files and sequence stubs based on sequence length data
           in MAF file

       --trust
           trust the comment annotation added by TBA on the second line of the file (if present)
           that it lists tree used in the alignment and all of the sequences involved. Defaults
           to on. use --notrust to distrust TBA tags (technically this data isn't part of the
           file format specification and is just crammed into comments that TBA produces, but
           might not be present or accurate on all MAF files, thus we give you the option to
           distrust it).

       --sort
           Sort the sequences found by --trust (so as to match the output that would have
           happened with --notrust).