Leandro Jones --
Nick's rules won't allways work in a Parsimony context. For example, a
position like this one:
1 A
2 A
3 T
4 C
would be informative under rules (a) and (b), but it is in reality
uninformative, as any of the possible trees have a length of 2. Thus,
this character tells
Hi all,
It can be done with phyloch but I forgot the name of the function.
HTH
Emmanuel
-Original Message-
From: Leandro Jones lrj...@gmail.com
Sender: r-sig-phylo-boun...@r-project.org
Date: Mon, 19 Sep 2011 07:35:32
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Show
Date: Sat, 17 Sep 2011 11:21:45 -0700
From: Jimmy O'Donnell jodonn...@biology.ucsc.edu
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Show Informative Sites?
Message-ID: f1a6d774-e4e2-4903-b959-61cb33612...@biology.ucsc.edu
Content-Type: text/plain; charset=us-ascii
Hi all,
A
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
Nick Matzke wrote:
All sites are informative under likelihood,
... and under Bayesian methods, and under distance matrix methods too. If you
leave out uninformative sites without compensating for doing that by an
explicit statistical correction, you will have some very unpleasant surprises.
