[ensembl-dev] apparent and low confidence orthology

[Julien Roux]

Dear mailing list,

I am wondering how to access information on the homology objects using 
the Compara API. In particular I would like to be sure that an orthology 
relationships I am looking at are not an "apparent" orthology 
relationships (reciprocal gene losses after a duplication event)
A few years ago, this info used to be included in the description() 
field (e.g., "apparent_orthology"), but it doesn't seem to be the case 
any more.
In the documentation I have seen the function is_tree_compliant(). What 
is it giving?
Also in Biomart, you can get an orthology confidence score [0 low, 1 
high]. What does it mean and how is it calculated? How do you access it 
using the API?

Last question: is there a score difference between an apparent orthology 
following a duplication node or following a dubious duplication node?

Thnaks for you help
Julien

-- 
Julien Roux
Marie-Curie postdoctoral fellow
Department of Ecology and Evolution, University of Lausanne, Switzerland
http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html
Tel: +41 78 700 2931