Friday, August 17, 2007
Bird supertree project - "Open Source" phylogenetics
Today is the day Katie Davis and I are launching the Bird Supertree Project. Partly an effort to distribute the task of building the tree, partly an experiment in "open source phylogenetics", we're curious (if not anxious) to see how this works out.
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5 comments:
Why not post a format with terminal labels that are friendly for programs such as TNT, i.e. with 32 or fewer characters in the label? Might have been wiser to prefix a unique ID before each name in that sense.
More anonymous comments- not sure if the labels are actually > 32 characters, need to confirm that, so perhaps the previous jumps the gun. Perhaps add fields to the results tracking that store 1) time taken to get the results (doesn't have to be precise) and 2) software used (again, just general information). These could be put in comments, but it seems like they should warrant their own fields.
Thanks for the comments. I've uploaded a Hennig86 formatted version of the matrix here.
I think the names are still unique at 32 characters. Personally I dislike numbers in labels, it makes the results hard to read (and we have enough problems with seeing the results as it is).
Regarding the form, yes there is a lot more that could be added to the form, I was trying to keep it simple. I'll look at adding some more fields as soon as somebody (anybody) starts uploading some trees.
Taxon labels are unique, but it will be an annoyance to rename the one taxon > 32 characters (Protocypselomorphus_manfredkelleri) when moving trees b/w PAUP/TNT etc.
While I'm sure it will be standardized on your side, you might want to mention some guidelines for calculating the reported score. For instance the k.davis tree calculates as to 18151 for me in PAUP*, not 18200.
Please obfuscate the email addresses on the results page, or allow people to obfuscate them on the upload form.
Matt, apologies for the delay, I've now obfuscated the email addresses. We'll look at the discrepancy in tree length.
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