Good day all,
I noticed something that I would consider an anomaly when analysing one
of my trees with NJ.
A 'polytomy' of samples contained many bootstrap values of 100 between
samples. I was looking at the total change in bootstrap values for all
nodes when I picked this up (as the signal in the data started to
disappear during subsetting, the number of nodes with bootstrap values
of 100 suddenly rocketed up).
Here's my best shot at reproducing my results in a standard way.
library(ape)
a <- as.DNAbin(matrix('a',10,10)) # DNA data with no variation
b <- dist.dna(a,mode='N')
c <- nj(b)
plot(c) #No surprises - a single polytomy
boot.phylo(tr, a, function(xx)
nj(dist.dna(xx[sample(1:nrow(xx)),],model="N")),B=100)
# Not what I expected - I would have thought all BS values would be 0
Am I missing something about how NJ is working in ape. If I perform a
similar analysis in PAUP none of the bipartions are greater than 12%,
which is what I would have expected, considering that there is no
information in the dataset.
Any help would be greatly appreciated.
Cheers,
Alastair
--
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Alastair Potts
PhD candidate
Botany Department
University of Cape Town
alastair.po...@uct.ac.za or pott...@gmail.com
University Private Bag, Rondebosch 7700, South Africa
or
PO Box 115, Loxton 6985, South Africa
Cell: 082 491-7275
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