[Biopython-dev] Parsing PAML supplementary output

[Eric Talevich]

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