[Biopython] generate phylogenetic tree

[Eric Talevich]

On Wed, Oct 30, 2013 at 7:22 AM, john fernando <fernando.j at inbox.com> wrote:

> Hi,
>
> first off, I am very new to the bioinformatics/biopython world so this may
> come as a naive question, so I apologize in advance.
>
> I extracted some sequences of PDB, aligned them using BLOSUM62 and have
> "scores".
>
> I was wondering if anyone can give tips/advice on I can set about
> generating a phylogenetic tree of the results to graphically show the
> clusters of similar sequences?
>
> I want to do this for my 'own' substitution matrix (next step).
>
> I am asking not necessarily code but more tools that people have used that
> can do this using the "scores" I have calculated.
> Thank you,
> John
>

Hi John,

To quickly get a tree to look at, given a multiple sequence alignment, I
recommend FastTree.
http://www.microbesonline.org/fasttree/

If you'd prefer a graphical program to start with, ClustalX and JalView are
both capable of building trees with a neighbor-joining algorithm, among
other things.
http://www.clustal.org/clustal2/
http://www.jalview.org/

To view a large tree and apply your own highlighting and colorization, try
Archaeopteryx.
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx

Back on the command line, some of the EMBOSS tools allow you to supply your
own scoring matrix, and so does Phylip, I think.
http://emboss.sourceforge.net/
http://evolution.genetics.washington.edu/phylip.html

If none of those work for you and you'd like to try building a tree from
your own distance matrix using Biopython, this is possible with Yanbo Ye's
recent work on another development branch:
http://biopython.org/wiki/Phylo#Upcoming_GSoC_2013_features
https://github.com/lijax/biopython/

Hope that helps,
Eric