Branch lengths estimation in RAxML

[Jose Barba-Montoya]

Dear Alexis,

I have a question about branch lengths estimation: 

If I use -q option (without option -M) for a partitioned analysis in RAxML, the model assumes proportional branch lengths among partitions, or all partitions share the same set of branch lengths, as in a concatenated analysis?

Thanks a lot for your help.

Best,

Jose

[Alexandros Stamatakis]

all branches share the same length,

alexis

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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