Dear community,
I have a sequence alignment (full 16S rDNA) and I'd like to calculate the sequence pairwise distance matrix using a nucleotide substitution model. The task could be easily achieved with the dist.dna() function of the R'package ape but there are not a lot of evolutionary model included (at least not the one I need). Indeed, screening my alignment with jModelTest I got that the best nucleotide substitution model for my data is TVM+I+G (invariable sites and rate variation among sites, respectively).
Does anyone know how I can get a distance matrix computed using this (TVM+I+G) substitution model?
Many thanks!
Luca