highest PAML version supported?

[Dave Messina-3]

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-3]

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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich@...
jason@...

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[Dave Messina-3]

Hi everyone,

I just committed support for parsing codeml 4.3a (August 2009) to bioperl-live. I added new tests and all PAML-related tests pass, but please report any problems you have to the list.

Note that I haven't tested the other PAML 4.3a executables to see if there are format changes with those. If you get the chance to try any and it doesn't work, let me know and I'll try to add support for them.

(Note that these changes are only to the PAML parsing code; Bio::Tools::Run already appears to handle 4.3a just fine.)


Dave


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