[Bioperl-l] tree comparisons with bioperl

Asher Cutter acutter at eeb.utoronto.ca
Thu Jul 19 22:25:08 EDT 2007


I was reading over the functions for working with trees in bioperl. I am 
looking for something that will compare two topologies and report back 
if they are equivalent. i.e. something like:

does ((a,(b,c)) == ((A,B),C) ? (in this case, no)

But of course in reality they would be more complicated topologies. This 
would be useful for simulating random trees to compare with some given 
topology of interest.

I saw the methods for testing for monophyly and paraphyly, but not much 
beyond that...perhaps I have missed something?

Any suggestions?

Thanks,
Asher

-- 

___________________________________
Asher D. Cutter
Assistant Professor
Department of Ecology & Evolutionary Biology
University of Toronto
25 Harbord St.
Toronto, ON, M5S 3G5

tel: 416-978-4602
email: acutter at eeb.utoronto.ca
http://www.eeb.utoronto.ca/faculty/faculty_profile.cfm?prof_id=130
___________________________________


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