Hi Marcelo,
unfortunately incongruence is not well defined. Here are several
possibilities to access incongruence,
with phangorn/ ape. I would first check if the base frequencies are similar
in each partitions.
There are a few exploratory tools for displaying incongruence like split
networks or the densiTree
to compare trees from different partitions.
More formally you can use a SH-test (SH.test) to test if trees or models
estimated for partitions differ.
Regards,
Klaus
On Tue, May 14, 2013 at 6:12 AM, Marcelo Reginato
reginato...@yahoo.com.brwrote:
Hi,
I'd like to know if anyone is aware of any tool in R to assess
incongruence among dna partitions.
Best,
Marcelo
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Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
http://darwin.uvigo.es/kschliep/
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