[Bioperl-guts-l] [Bug 2636] New version of PAML changes output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Nov 16 00:51:38 EST 2008


------- Comment #5 from cjfields at bioperl.org  2008-11-16 00:51 EST -------
Again, it would help tremendously to have example files to work with.  I don't
see this being resolved until after 1.6 is released.

(In reply to comment #4)
> I've found another line changing on the PAML output (although I think it
> already happened on older versions).
> When you suply a newick tree with branch lengths and those values are fixed
> during PAML analysis (fix_blength = 2) the branch line (eg. "6..7     7..8    
> 8..1     8..5     7..2     6..3     6..4") is omited from output. If this line
> is not present on the mlc file, PAML.pm cannot correctly identify existing
> branches and fails to output a correct tree.
> I tried to fix it but it involved too much tweaking and I was affraid my
> changes would have nastier side effects. To temporarily overcome this bug I've
> changed the PAML source code file "codeml.c" at line 752 (v4.1) from 
> "if(com.fix_blength<2) {  OutTreeB(fout);  FPN(fout); }"
> to
> "if(com.fix_blength<=2) {  OutTreeB(fout);  FPN(fout); }"
> I'll post this sugestion to Yang on GSF, also.

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