All sites are informative under likelihood, but I assume you
mean parsimony-informative, in which case all you have to do
is count which sites are either (a) uniform or (b) uniform
except for differences found only in a single species.
Probably easiest if you convert the read.nexus.data output
to a dataframe with as.data.frame, then use unique and == to
count the number of states in each site...
On 9/17/11 11:21 AM, Jimmy O'Donnell wrote:
Hi all,
A simple question to which I can't seem to find an answer: is there a way to
show only the informative sites of a DNA sequence dataset in R?
Thanks,
Jimmy
--
Jimmy O'Donnell
PhD Candidate
Ecology and Evolutionary Biology
University of California
Santa Cruz, CA 95060
jodonn...@biology.ucsc.edu
(407)744-3377
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Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
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Principles of Phylogenetics: Ecology and Evolution
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When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
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view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
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