[Bioperl-l] Re: Comparative genomics

[David J. States]

--On Friday, September 28, 2001 11:56 AM +0100 Elia Stupka <elia@ebi.ac.uk> 
wrote:

> It turns out that phylogenetic trees have a nice flatfile format, and can
> be parsed. We'll write the db schema, object layer,etc. to store those
> phylogenetic trees in the db. Please shout if similar things exist
> already, I am thinking of adding them to bioperl.

You will need several representations:
-- tree topology alone
-- a tree annotated with branch lengths or node weigths
    -- parsiomony, # of changes
    -- ML, evolutionary distance
    -- consensus trees (possibly not binary)
-- a collection of alternative trees (e.g. Phylip/PENNY)

All of these can be accommodated in the nested parenthesis notation, but 
for large families or large collections of trees, the strings may get quite 
large.

In addition, it would be worth allowing for a description of the method 
used to generate the tree(s).

David

David J. States, M.D., Ph.D.
Professor of Human Genetics
Director of Bioinformatics
University of Michigan School of Medicine
Medical Science Building II, Room 5622A
Ann Arbor, MI   48109
USA
email: dstates@umich.edu
tel: (734) 615-5510
fax: (734) 615-6553
URL: http://stateslab.bioinformatics.med.umich.edu