[Bioperl-l] extending the PHYLIP format
avilella at gmail.com
Wed May 28 06:31:07 EDT 2008
About a year ago, some code was added to deal with "the more than 10 chars"
Basically: (1) mapping the long ids to 10-char numeric ids, (2) running the
with the id limitation, (3) reverting the ids back to the originals in the
output. The pods explain how to do it.
So I would say that the solution is at least "partially" there :-)
On Wed, May 28, 2008 at 9:23 AM, Heikki Lehvaslaiho <heikki at sanbi.ac.za>
> I just learned that a number of phylogenetics packages (PAUP, PHYML, Mr
> at least ) now allow longer than 10 character IDs in PHYLIP format. The
> documentation is scarce but the rules seem to be:
> 1. There can be spaces before the ID.
> 2. The ID can be up to 50 characters long.
> 3. ID can contain any characters. If you are using spaces within the ID,
> have to put the whole ID in single quotes ('). Single quotes can be used
> all IDs and are removed when parsing in.
> 4. It is customary to have two spaces between the ID and the sequence.
> This custom seems to have come into PHYLIP format from Nexus.
> Note that this allows sequences in a file to start at different columns.
> Can anyone shed more light into matter?
> I need to get this into bioperl as the names in HIV sequences that I work
> are very long and can not be sensibly truncated.
> What would be the best way to do this?
> 1. Add more options to the already heavily
> hacked Bio::AlignIO::phylip.pm
> 2. Create a Bio::AlignIO::phyliplong.pm
> Do those ugly hacks for supporting fixed length long IDs really really
> in the vanilla phylip.pm file?
> ______ _/ _/_____________________________________________________
> _/ _/
> _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
> _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho
> _/ _/ _/ SANBI, South African National Bioinformatics Institute
> _/ _/ _/ University of Western Cape, South Africa
> _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
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