[Biopython] Request from help

[Eric Ma]

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?

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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