[BioPython] Creating and traversing an ultrametric tree

[Peter]

On Wed, Sep 24, 2008 at 1:13 AM, aditya shukla
<adityashukla1983 at gmail.com> wrote:
> Hello Folks,
>

Hi Aditya,

>
> Can someone explain how can an ultrametric tree be  created and traversed?
>

What kind of data are you starting with?  People tend to use
specialist software to generate trees using a range of algorithms,
often starting from a set of aligned sequences.

>
> I found think link on ultrametric trees but didn't get a lot from it.
> http://www.koders.com/python/fid414AE4B3075F9E434B76B0AEA3CE336C5A9F60F8.aspx?s=cdef%3Atree#L4
>

Its a shame that code doesn't seem to include a header with any
copyright or authorship statement.  It is not using Biopython, and my
initial guess was the "import newick" was using Thomas Mailund's
Newick tree parser: http://www.daimi.au.dk/~mailund/newick.html (You
can alternatively use the Bio.Nexus module in Biopython to parse a
Newick tree)

However, clicking on some of the other neighbouring files on that
koders.com website I realised you are looking at a copy of the
lagrange python package ("Likelihood analysis of geographic range
evolution"), the homepage for which is here:
http://code.google.com/p/lagrange/

Peter