all by all phylogenetic distances for massive set of ncbi taxon ID's
0
1
Entering edit mode
5.9 years ago
bioguy ▴ 50

Any ideas on how to extract phylogenetic tree distances/dissimilarity for a massive group of ncbi taxonomic ids, like 50-100K? Ideally I'd be able to generate or download a file of the form:

Taxa1,Taxa2,Distance
Taxa1,Taxa3,Distance

......

This was the closest thing I could find (https://www.biostars.org/p/312148/), but it seems to require doing it in R, and I'm pretty sure R can't handle matrices of the scale I'm thinking.

phylogeny microbiology taxonomy ncbi taxon id • 1.8k views
ADD COMMENT
2
Entering edit mode

I think you can use the ETE3 toolkit to generate a tree representation of NCBI taxid's (you can give it a hierarchy level I think (e.g. primates) and get all the taxa below it) and calculate all-vs-all inter-tip distances (I have some code which can do this last bit, but no idea how it'll scale).

ADD REPLY
0
Entering edit mode

ok cool, this helps a lot, thank you. Giving it a shot now, we'll see how it works out...

ADD REPLY

Login before adding your answer.

Traffic: 1997 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6