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).

perl v5.40.0                                       2024-11-30                                     MAF2ANCHORS(1)