[Biopython] Codeml parser in Biopython?

natassa natassa_g_2000 at yahoo.com
Mon Sep 13 16:22:26 UTC 2010


Hello, 
I was wondering if there  is a Biopython solution to parsing codeml results from 
paml. the output files are pretty standard, so such a parser should be quite 
straightforward to write up. I d volunteer for this, but thought I might check 
first if somebody else has done this. Actually, I found a read-only pypaml 
interface in google codes, tried it out and realized I had to edit several 
things to even import it (in python 2.5), which is quite strange: It was mainly 
built-in methods that throwed errors..Anyway, i 'corrected' this and then 
realized that the output files assumed by this code may not be the same as mine, 
although again, the outputs of codeml are pretty standard. I am not sure how 
much this code is used and was not sure what is the developper's email to ask 
him some questions. 

I am interested in parsing outputs from Branch, Site and BranchSite models, so 
everthing that codeml can do. Any information by experienced users is welcome!
Thanks, 
Anastasia Gioti



      



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