I have constructed a distance matrix in order to produce a phylogenetic tree for 10 species in R package 'phangorn' and I would like to know how can I calculate p-values for significantly different species based purely on phylogenetic data. I would appreciate some insight, especially by the ones who have tried anything similar with 'phytools'.
you can try Bootstrapping, you can choose number of bootstraps, with this you can observe how many resampling would give the similar tree you are expecting. consequently , you can calculate p-values too
there is nice package in R that does the needful
its called pvclust its here