Entering edit mode
Nora Muda
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70
@nora-muda-2065
Last seen 10.2 years ago
Thank you to Martin and Earl for their response and
answered.
I got answered from Emmanuel Paradis. Below are the
solutions:
'boot.phylo(phy,x,FUN,B=100,block=1)'
x is a character matrix (not the distance matrix) that
will be resampled for the bootstrap.
My mistake is not to store the tree which is needed by
boot.phylo; so
tr <- nj(distallbacteria)
Therefore;
boot.phylo(tr,allbacteria,FUN=function(xx)nj(dist.dna(xx,pairwise.dele
tion=TRUE)
We also can refer to the book on using R for
phylogenetic analyses, written by Emmanuel Paradis :
http://www.springer.com/west/home/statistics/stats+life+sci?SGWID=4-10
134-22-156993712-0
--Nora.
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Dear Nora, I have a similar problem.
I tried different inputs for the parameter x of boot.phylo (raw seq, msa object), but they did not work. Could you please give me an example of x's structure? Thank you very much for your help