[Bioperl-l] Re: Comparative genomics - tree annotation

[David J. States]

--On Friday, September 28, 2001 2:46 PM +0100 Elia Stupka <elia@ebi.ac.uk> 
wrote:
> What annotation will be associated with each node of the tree.
> Do you think the annotation will always be associated to
> each individual node, or should we allow for both
> whole-tree annotation and individual node annotation?

Potential node level annotation
- fraction of trees with this node as a consensus clique
- consensus sequence
- divergence date, infered and w/ reference to fossile record
- links to nodes in taxonomic trees

Potential whole tree annotation
- alignment method (program, version, parameters)
- tree building method (program, version, parameters)
- summary of manual inputs and constraints applied
- summary of the sequence set (why choosen, taxa, function)
- whole sequence vs. domain vs. mixed

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