Re: [R-sig-phylo] Average Aminoacid Identity tree with bootstrap support. Is it possible?

2017-04-07 Thread Joe Felsenstein 
Salvador Espada Hinojosa --

The problem, of course, is that a random substitution on an interior
branch of a tree increases or decreases the size of more than one
distance in the distance matrix.  The distances aren't independent in
their statistical noise.  So you can't just sample distances after the
distance matrix is computed.

J.F.

Joe Felsenstein j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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Re: [R-sig-phylo] Average Aminoacid Identity tree with bootstrap support. Is it possible?

2017-04-07 Thread Emmanuel Paradis 

Hi Salvador,

You first need to define the variables that would be resampled during 
the bootstrap procedure. In the case of DNA sequences, this would be the 
columns (= sites) of the alignment, since they each contribute to the 
distance calculation (or to the likelihod function if you use ML). So 
you have to find the equivalent for your genomic data (my intuition 
tells me that won't be straightforward...)


Once you did that, you can arrange these variables into a matrix (or 
data frame) and input it into boot.phylo with the NJ tree.


HTH.

Best,

Emmanuel

Le 06/04/2017 à 16:44, Salvador Espada Hinojosa a écrit :

hello,

I'm PhD student and I have genomic bacterial data and want to produce a
tree from it. I'm currently using around 10 genomes and I calculated their
"Average Amino acid Identity" so I have the distance matrix
(distance=1-AAI). I produced with ape a neighbor joining tree, and wanted
to produce bootstrap support. Since I feed R with the distance matrix, I
cannot use the command boot.phylo, that requires "a taxa (rows) by
characters (columns) matrix" as one of the inputs.

Could you give me any suggestion, please?

Thanks a lot!



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