[Bioperl-l] extending the PHYLIP format

Chris Fields cjfields at uiuc.edu
Wed May 28 09:51:55 EDT 2008


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).

chris

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 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
>
> -- 
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>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
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>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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