Fwd: NeXML question

[Rutger Vos]

Dear Laszlo,

thank you very much for putting this question to me, it was actually a topic I was planning to expand on a little bit anyway. I've had to fix a bug in Bio::Phylo to make what you're trying to do a little bit easier, and have uploaded the new version that fixes this to CPAN. The version number is 0.48, which should be available on your CPAN in a few hours (I just checked: not yet).

I wrote a blog post / tutorial that discusses how you would annotate individual characters, write the result to NeXML and read that back in for further analysis. The blog post is here: http://biophylo.blogspot.com/2012/05/reading-and-writing-complex-character.html

Note that NeXML (and indeed all XML) is rather verbose so there is an upper limit to how large your data matrices can be, but if you find this a promising avenue please do give it a try, and if you run into any problems let me know and perhaps I can optimize the code a little. Perhaps it's fine though: I've had no problems reading the entire ToLWeb tree (and the entire TreeZilla alignment) as NeXML so maybe it's not an issue.

Best wishes,

Rutger

---------- Forwarded message ----------
From: Laszlo Nagy
Date: Tuesday, May 1, 2012
Subject: NeXML question
To: "rutge...@gmail.com" <rutge...@gmail.com>


Hi Rutger,

I am about to implement a workflow in perl, which should store a high number of discrete characters and associated information in a file for later access. I am hesitating between the nexus and nexml standard (the latter accessed from Bio::Phylo), being much less familiar with the latter. The bottleneck in my work is that characters preferably have to be written and later accessed one by one, which makes several methods that handle bigger alignment-like chunks of characters infeasible. The other point is that each character has a bunch of information associated with it, which should be retrievable after analysis. I would not really feel comfortable with storing all characters in a hash and writing them all together (partly due to the size of the final matrix) Do you think nexml has significant advantages with regard to these two aspect as compared to nexus? Is there a tutorial for using the Bio::Phylo::NeXML methods?

Thank you in advance!

cheers,
Laszlo

Btw, congtatulations to the Bio::Phylo package, I find it very handy, for me works better than the core phylo methods of BioPerl!

Postdoctoral Researcher
http://www.clarku.edu/faculty/dhibbett/people_Laszlo.html

--
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com