Dear John,
John Cumbers wrote on 25/06/2011 14:00:
Dear all,
Do you know if there an easy way to convert phylogenetic trees into
the distance matrix files that CADM takes as input?
You can compute these matrices with cophenetic, then concatenate them
into a single matrix with rbind after eventually reordering them so that
the columns match, eg:
a <- rtree(5)
b <- rtree(5)
A <- cophenetic(a)
B <- cophenetic(b)
rownames(A) == rownames(B)
[1] FALSE TRUE FALSE FALSE FALSE
x <- rownames(A)
B <- B[x, x]
M <- rbind(A, B)
CADM.global(M, 2, 5)
The help page is not clear on this point. I'm Cc'ing to Pierre Legendre
(I guess this is borrowed from a previous stand-alone program).
Alternatively, what other statistical congruence tests do you
recommend to demonstrate whether the trees obtained by different
markers are significantly different, and whether it is valid to
concatenate them together into a single alignment?
If you analyze sequences, phangorn allows you to define partitioned
models. You can then computer LRT comparing different models. See the
function pmlPart in this package.
Best,
Emmanuel
Best,
John
Brown U.
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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