This is the command maf2anchors.pl that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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).
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