[Bioperl-l] extending the PHYLIP format

Heikki Lehvaslaiho heikki at sanbi.ac.za
Wed May 28 04:23:51 EDT 2008


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 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 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?

Opinions?

	-Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  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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