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>