[Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs?
jason.stajich at duke.edu
Tue Nov 1 19:08:28 EST 2005
That's right. see the PAML HOWTO - $dna_aln can be slices of an
# set the alignment object
# run the KaKs analysis
my ($rc,$parser) = $kaks_factory->run();
my $result = $parser->next_result;
my $MLmatrix = $result->get_MLmatrix();
On Nov 1, 2005, at 7:00 PM, Bingshan Li wrote:
> Thanks, Jason, for this reply and the other for Ganbank parser. For
> Yn00, can we pass a slice of alignment to it so that I can
> calculate ka/ks for sliding windows? I ran PAML as a stand alone
> program but never used it in perl script.
> Thanks a lot!
> On Nov 1, 2005, at 4:45 PM, Jason Stajich wrote:
>> I suggest Codeml and YN00 - I assume you are only doing this for
>> pairwise comparisons and not along a tree?
>> The dnastats module calculates Nei-Gojobori so it will be
>> different, but shouldn't be that different so something must be
>> wrong with your code or the module's method. Maybe you can post a
>> bug to bugzilla.open-bio.org with a clear example of where it is
>> going wrong and we'll take a look.
>> I would just use YN00 for most pairwise - you can parse it with
>> Bio::Tools::Phylo::PAML and automate running it with
>> On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote:
>>> Hi all,
>>> I used Bio::Align::DNAStatistics module to calculate ka/ks ratio
>>> but I found the result is very different from the output by yn00
>>> in PAML 3.14. I applied "calc_KaKs_pair" function on two
>>> sequences to test it. The difference is pretty big (for one case
>>> it gave ka/ks=1.35 while yn00 gave 0.37). Does anybody have same
>>> experience? Is there any other methods I can use to calculate ka/
>>> ks ratios? I will also use it to calculate ka/ks in sliding windows.
>>> Thanks a lot!
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>> Jason Stajich
>> Duke University
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