aln2aln - convert different alignment formats to another alignment format
perl aln2aln.pl [OPTIONS] [--help] <input_alignment_file> <file_in_other_format>
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.
If the sequence ids from the input alignment are too long, take the last 10 characters of the id.
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
Bio::AlignIO
jw bargsten, <joachim.bargsten at wur.nl>
<joachim.bargsten at wur.nl>
To install Bio::Gonzales, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Gonzales
CPAN shell
perl -MCPAN -e shell install Bio::Gonzales
For more information on module installation, please visit the detailed CPAN module installation guide.