[Biopython-dev] Parsing PAML supplementary output

[Peter Cock]

On Tue, Oct 11, 2011 at 1:55 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Tue, Oct 11, 2011 at 6:13 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> That looks like exactly the kind of issue NEXUS was designed
>> to solve: how to embed alignments, trees and other stuff into
>> a single plain text file for input into a phylogenetic tool.
>>
>> Doesn't PHYLIP have an XML format these days? Trying
>> to parse something like that text (without a formal standard)
>> seems like a painful exercise and long term maintenance
>> headache.
>>
>
> The Phylip programs seqboot and retree have XML formats that look almost
> like SeqXML and phyloXML, but they're not quite compatible, e.g. attribute
> names are slightly different.
>
> This is probably because they were written before those standard formats
> existed -- pretty sure the retree XML format, sort of described in Inferring
> Phylogenies (2004) as an example of how a future XML tree format might look,
> was an inspiration for phyloXML. There hasn't been much development on these
> parts of the Phylip codebase lately, though. If someone wanted to write a
> patch to bring these formats into compliance with the closest standards, I
> bet Joe would accept the patch.
>
> Discussion:
> https://www.facebook.com/permalink.php?story_fbid=256082801069968&id=115402811804635
>
> -E

Good plan - anyone here familiar with the PHYLIP code base?

Peter