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.




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

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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