[Bioperl-l] nucleotide changes along tree

[Chris Fields]

+1 on all this, just wish the output were easily parsable from version to version :P

chris

On Feb 1, 2011, at 8:21 AM, Gregory Jordan wrote:

> Hi Nicholas,
> 
> PAML is the de facto standard for ancestral reconstruction of DNA
> sequences. http://abacus.gene.ucl.ac.uk/software/paml.html
> 
> <http://abacus.gene.ucl.ac.uk/software/paml.html>BioPerl contains a
> Bio::Tools::Phylo::PAML module for running PAML and parsing the output.
> There's a how-to (http://www.bioperl.org/wiki/HOWTO:PAML) and documentation
> on the specific methods to access ancestral state reconstructions (
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Tools/Phylo/PAML/Result.html#Synopsis)
> .
> 
> If you're just doing a one-off run and don't need to automate things, you
> may be better off running PAML on its own. Extensive documentation is
> available from the PAML site (first link above).
> 
> Cheers,
> Greg
> 
> On Mon, Jan 31, 2011 at 4:30 PM, Nicholas Price <price4890 at gmail.com> wrote:
> 
>> Hi
>> 
>> I have  three nucleotide sequences from human, chimp and Orangutan and
>> the corresponding tree.I want align the sequences and for each column
>> in the alignment where there are substitutions, I want to infer on
>> which branches the changes occurred using a maximum likelihood method.
>> Is there a way to do this in Bioperl??
>> 
>> thank you
>> 
>> Nicholas
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