Hi Alastair,
it is not that surprising. NJ normally does not produce poytomies,
just edge weights of length 0. How these are broken may depends from
the input order (from labels in the distance matrix like in this
implementation) or could be broken randomly. I added some code below
to highlight it.
However you can use the function di2multi to produce real
multifurcating trees.
Cheers,
Klaus
On 5/5/11, Alastair Potts <pott...@gmail.com> wrote:
> 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
That is wrong the tree has all internal edges, just the edge length are 0.
If you count the tree is fully resolved
> c$edge.length
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
c$edge.length[] = 1 # I don't add edges, just change the edge length
plot(c)
> 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
>
>
>
>
> --
> -----------------------------------------------------------------
> 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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>
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--
Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris
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