[Biopython] generate phylogenetic tree

[George Devaniranjan]

While I have never used PHYLIP a lot , I would really recommend their
FAQ's, they give some great resources (both online and books ) to get you
started.
Eric has given some great tips too, hopefully all this will be of help to
you-Good luck.


On Thu, Oct 31, 2013 at 5:38 PM, Eric Talevich <eric.talevich at gmail.com>wrote:

> 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
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>