[Biopython] Request from help

[Paulo Nuin]

On 2013-04-11, at 12:49 PM, Eric Ma <ericmajinglong at gmail.com> wrote:

> Hello everybody,
> 
> I'm new to the mailing list here, though I've been playing with BioPython
> for quite a while.
> 
> I'm having some trouble here. I wanted to display a tree of sequences for
> which I had done a multiple sequence alignment. I tried going through the
> pipeline example here (http://biopython.org/wiki/Phylo#Example_pipeline).
> Because I'm still in the testing phase, instead of writing it as a single
> script, I wrote it as a series of scripts that I would execute in order.
> 
> The problem I run into is at step 4 in the example, where I "feed the
> alignment to PhyML". My data set is 70 protein sequences, and the trouble I
> run into is that it takes a very, very long time at the "feeding alignment
> to PhyML" step. I tried running the script on my MacBook Pro overnight, and
> even the next morning it was not done. Am I missing something here?
> 

Hi

With 70 OTUs you have 5.00 E115 possible trees. Guaranteed it will take a long time, independent to what parameters you are using in PhyML. Try with a smaller number of taxa, just for testing purposes and depending on the complexity of your protein phylogeny, give your computer some weeks to actually generate some result.

This is not a BioPython issue, is more a phylogenetics one.

Cheers
Paulo





> Just to be clear here, aligning the sequences using Muscle was successful,
> and I also managed to output a distance matrix from sample to sample, which
> I used in another downstream pipeline to display the clustering of the
> sequences on a 2D euclidean plane. However, I wanted to have a tree
> representation to validate the clustering results; the trouble is, I can't
> get the _phyml_tree.txt file to be created, which I would then use to draw
> the tree.
> 
> Thanks in advance for any help!
> 
> Cheers,
> Eric
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