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willpearse / phyloGenerator

Automated Phylogeny Generation for Ecologists
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Controlling for phylogeny in a comparative life-history study #1

Closed abaxter closed 12 years ago

abaxter commented 12 years ago

I'd like to use your program to obtain family and order classification for around 2500 bird species across most of the 143 families identified by Sibley & Ahlquist (1990). I already have classification to genus level but anything else time saving would be fantastic!

Any help would be great!

Alistair Baxter

willpearse commented 12 years ago

Hello,

To actually get the genus/family level assignments (other than using the actual book...) you could use the GenBank taxonomy. I'm just about to put that up, so give it a try then.

Cheers,

Will

willpearse commented 12 years ago

I've put what I think will help in the experimental branch 'taxonomy'. Something like this:

./phyloGenerator.py -taxonomyLookup test_taxonomy.txt -name test -timeout 10 -email will.pearse@gmail.com

...should do the job. I'll be linking this isn't a contraint-tree generating bit for the whole thing soon.

HTH

Will