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

[kevin fan]

hi, Chris and Dave,

i will try to get permission from the boss. since the sequences i mentioned
are from a new species.

kevin.

2009/2/9 Chris Fields <cjfields at illinois.edu>

> kevin,
>
> As Dave mentioned, go ahead and attach any output from PAML 4.2 to the bug
> report.  I want to make it a priority to get the PAMLM parser working for
> the 1.6 release series (if not 1.6.1, maybe 1.6.2).
>
> chris
>
>
> On Feb 9, 2009, at 7:39 AM, kevin fan wrote:
>
>
>> hi, chris
>> thank you for the reply. i will use PAML 3.15 instead
>>
>> cheers,
>> kevin
>> 2009/2/9 Chris Fields <cjfields at illinois.edu>
>> 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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>>
>