[Bioperl-l] highest PAML version supported?

[Jason Stajich]

prolly 3.15 or so.

it really needs a maintainer!!!

On Nov 12, 2009, at 11:20 AM, Dave Messina wrote:

> 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
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org