[Bioperl-l] extending the PHYLIP format
jason at bioperl.org
Wed May 28 13:28:50 EDT 2008
Should also ask Weigang what the status is, I think he implemented a
lot of it.
On May 28, 2008, at 6:51 AM, Chris Fields wrote:
> Could you post a few example phylip sequences with long names to
> svn and add a ticket to bugzilla? I would consider this a somewhat
> high-priority enhancement.
> I think keeping this in a single phylip module would be best, but
> we'll to see how feasible it is. I think it is possible to do so,
> however, and still retain some backwards compatibility (I may even
> have an idea how, just need to test it out).
> On May 28, 2008, at 3:23 AM, Heikki Lehvaslaiho wrote:
>> I just learned that a number of phylogenetics packages (PAUP,
>> PHYML, Mr Bayes
>> 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, you
>> have to put the whole ID in single quotes ('). Single quotes can
>> be used for
>> all IDs and are removed when parsing in.
>> 4. It is customary to have two spaces between the ID and the
>> This custom seems to have come into PHYLIP format from Nexus.
>> Note that this allows sequences in a file to start at different
>> Can anyone shed more light into matter?
>> I need to get this into bioperl as the names in HIV sequences that
>> I work with
>> 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 belong
>> 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
>> ___ _/_/_/_/_/
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
> Bioperl-l mailing list
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