Estimating P-Invar for some partitions in AA dataset

[Michael Forthman]

Hello,

I have an 80-gene AA matrix that has 19 partitions (best partitioning scheme determined by PartionFinderProtein). Some, but not all, of these partition include P-Invar. I wondering if

this can be specified in the partition file as, e.g., LGI, gene1 = 1-50. Or would the alternative be to select the "Estimate proportion of invariable sites (GTRGAMMA + I)", which, if I understand correctly, would apply to all partitions?

Thanks, Michael

[Alexandros Stamatakis]

Dear Michael,

This is unfortunately not possible, you can only chose one model of rate
heterogeneity which is then applied to all partitions.

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

[Michael Forthman]

I had thought so, but just double-checking. Thank you for answering my question! Cheers, Michael