Joachim Bargsten > Bio-Gonzales > aln2aln

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NAME ^

aln2aln - convert different alignment formats to another alignment format

SYNOPSIS ^

    perl aln2aln.pl [OPTIONS] [--help] <input_alignment_file> <file_in_other_format>

DESCRIPTION ^

Takes <input_alignment_file> and converts it to <file_in_other_format> On default, it assumes 'fasta' as input format, but you can use the --from option to make sure that aln2aln uses a different format. Same applies to --to

Some formats have a limitation on identifier length (>30 characters or so), so check this first, if strange problems occur.

OPTIONS ^

--shorten-id-from-end

If the sequence ids from the input alignment are too long, take the last 10 characters of the id.

--from <FORMAT> and --to <FORMAT>

Assume one of the following alignment input formats:

FORMATS:

    fasta       FASTA format
    pfam        pfam format
    selex       selex (hmmer) format
    stockholm   stockholm format
    prodom      prodom (protein domain) format
    msf         msf (GCG) format
    mase        mase (seaview) format
    bl2seq      Bl2seq Blast output
    nexus       Swofford et al NEXUS format
    pfam        Pfam sequence alignment format
    phylip      Felsenstein's PHYLIP format
    clustalw    ClustalW format

SEE ALSO ^

Bio::AlignIO

AUTHOR ^

jw bargsten, <joachim.bargsten at wur.nl>

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