[Bioperl-l] nucleotide changes along tree

[Gregory Jordan]

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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