SATe II versus RAxML Performance for megalarge datasets

[Robert Lucking]

Hi Alexi

I have a question that you might be able to answer: what is your feeling of computational time of SATe II versus RAxML for very large datasets, e.g. 16,000 ITS sequences (500 bases long)? If both could run on a cluster (e.g. Cipres with 64 cores), would SATe II be substantially slower or can it even handle that many sequences? Or would it be comparable?

Regards

[Alexandros Stamatakis]

Hi Robert,

It would more or less be comparable, i.e., just take proportionally
longer than RAxML. The reason for this is that it actually uses RAxML
for building trees and identifying subtrees whose sequence are aligned
using MAFFT and which are subsequently aligned to each other based on
the RAxML tree via a profile profile alignment.

Hope this helps,

Alexis

>
> Regards
>

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org