[Jalview-discuss] Re: JalView and Phylip output

[James Procter]

Hi Sebastian.

Thanks for the email. I've forwarded this to the jalview-discuss list
because I suspect this is of general interest.

Sebastien Moretti wrote:
> Do you plan to add a phylip format output to Jalview ?
it wasn't planned originally. Our preferred route for phylogeny
calculations was to pass the alignment to TOPALi (www.topali.org) or use
phylogeny web services (which don't exist as yet).

> I know that there is a 'problem' with the fact that strict phylip format
> must have sequence names cut to the 10th characters. 
yep - its only a problem if you care about the names - there would have
to be some user investigation concerning that. jalview doesn't need
unique names (in principal), but the tree-matching display requires
unambiguous correspondence. If phylip analyses were implemented via a
web service then all of that kind of housekeeping could  be hidden away
from the user.

> But, now, more and more software, like PhyML or PAML, use names longer
> than 10: 30 for PAML, no limit (?) for PhyML.
true. They still require unique names, however.

> What do you think to add a strict phylip format output and a non-strict
> one ?
It would be of use - but a switch would be needed between the strict and
non-strict when generating a PHYLIP formatted aligment. Otherwise, from
the looks of the format,
(http://evolution.genetics.washington.edu/phylip/doc/sequence.html) it
would be a very easy implementation since it is practically the same as
PFAM (except for the interleaved/not interleaved aspect).

> Do you know when the release with AMSA format support will be available ?
The jalview paper is still being written, and we originally planned to
delay the release of 2.4 until after it was submitted. However, I
suspect the 'official' release may happen before that now.

thanks for the mail!
Jim

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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