[Bioperl-l] met a problem when run Bio::Tools::Run::Phylo::PAML::Yn00

[Chris Fields]

We do not adequately support PAML v4.0 and up at this time.  Much of  
this is due to PAML's constantly shifting output (every release seems  
to break our parsers).

chris

On Feb 9, 2009, at 5:57 AM, kevin fan wrote:

> Dear all,
> i am using Bio::Tools::Run::Phylo::PAML::Yn00  to calculate Ka/Ks  
> ratio of
> pairwise sequences.
> bioperl version is 1.6, and PAML version is 4.2
>
> when i run the Bio::Tools::Run::Phylo::PAML::Yn00 , it warns:
>
> -------------------- WARNING ---------------------
> MSG: There was an error - see error_string for the program output
> ---------------------------------------------------
>
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Unknown format of PAML output did not see seqtype
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:359
> STACK: Bio::Tools::Phylo::PAML::_parse_summary
> /usr/local/share/perl/5.10.0/Bio/Tools/Phylo/PAML.pm:441
> STACK: Bio::Tools::Phylo::PAML::next_result
> /usr/local/share/perl/5.10.0/Bio/Tools/Phylo/PAML.pm:257
> STACK: kaks.pl:10
> ----------------------------------------------------------------
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