[Bioperl-l] PAML3 vs 4

[Jason Stajich]

Small tweaks were needed to parse PAML4 results.

Pairwise Ka, Ks parsing (runmode -2) should be working more smoothly  
now on both PAML 3 and 4.
You'll need to get the latest code from CVS in order to see the  
changes to Bio/Tools/Phylo/PAML.pm

I've added tests for PAML4 in the parser and the run code.

If you have scripts that use codeml please give it a try.  I have not  
attempted to play with BASEML or AAML results at this point so if you  
also have codes that use those programs, please try it out and  
provide bugreports if we need to fix things.

-jason

--
Jason Stajich
jason at bioperl.org