In article <7pbpqe$sc5 at net.bio.net>,
Julian <julian.robinson at plant-sciences.oxford.ac.uk> wrote:
>I have two data sets, one nuclear (ITS) and one cp (matK). I wish to test to
>see if they are incongruent or congruent. I think I'm up to speed on the
>literature etc. but I cannot find a description of how to implement the test
>in a programme, e.g. PAUP.
There is some discussion of these tests, in a likelihood context,
in the PHYLIP documentation for the program DNAML. It also has
pointers into the relevant literature. Look for the discussion of
the "Kishino-Hasegawa-Templeton test".
PAUP* can also do it but I don't know the documentation well enough
to give you a pointer there.
Mary Kuhner mkkuhner at genetics.washington.edu