constraint tree topology analysis using RAxML

[yl...@umich.edu]

I was running an analysis on Cipres using RAxML-HPC2 on XSEDE (7.4.4) using "Constraint (for monophyly)" and "Let RAxML halt bootstrapping automatically".  However, the constraint was ignored.  When I ran an analysis with "Specify an Explicit Number of Bootstraps" on, the constraint was effective.  Did I make any mistake or is there a bug in the software?

Thanks,

Yin-Long Qiu

[Alexandros Stamatakis]

I don't think that there is a bug, typically users have problems in
understanding the constraint tree option in RAxML, please search the
forum for previous discussions on this ...

If you still believe that the output is erroneous, please send me all
input files such that I can check.

Alexis

--
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