[Bioperl-l] highest PAML version supported?

[Dave Messina]

Hi everyone,

What is the latest version of PAML (specifically codeml) that I can use with
bioperl-live and bioperl-run?

I looked around and couldn't find where (or if) this is documented.


With PAML version 4.3a against the current trunk of both -live and -run I
see this:
------------- EXCEPTION Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK Bio::Tools::Phylo::PAML::_parse_summary
/Users/dave/src/bioperl-live/Bio/Tools/Phylo/PAML.pm:461
STACK Bio::Tools::Phylo::PAML::next_result
/Users/dave/src/bioperl-live/Bio/Tools/Phylo/PAML.pm:270
STACK toplevel ../bin/cluster_kaks:251
---------------------------------------------------------------

...which I suspect (but haven't confirmed) is due to a change in the file
format.


Dave