Re: [R-sig-phylo] mean phylogenetic distance for subsets of species from a tree

Hi Zach. Do you just mean the mean patristic distance among all pairwise combinations of species in each assemblage? If you have your assemblages in a list of vectors, each containing the species of the corresponding assemblage, I think you could do: library(ape) D<-cophenetic(tree)

[R-sig-phylo] mean phylogenetic distance for subsets of species from a tree

Hi everyone, I have a time-calibrated phylogeny with ~100 species and a list of ~1000 observed species assemblages which vary from 2-20 species in size. I'd like to get the mean phylogenetic distance among species in each assemblage, but I'm having difficulty finding a way to do this. The

Re: [R-sig-phylo] HKY GTR distances

Can you do this in MEGA? Jake > On Feb 1, 2017, at 5:52 PM, kolte...@rub.de > wrote: > > Dear Phylothusiasts, > I need to compare multiple substitution models side-by-side (species > clustering stuff by distances only). Unfortunately, I am not aware of an >

[R-sig-phylo] HKY GTR distances

Dear Phylothusiasts, I need to compare multiple substitution models side-by-side (species clustering stuff by distances only). Unfortunately, I am not aware of an implementation of HKY and GTR distance computations using R. Maybe there is some Github code or something else that I have been

[R-sig-phylo] detect psbA-trnH inversions (and what to do with them) before phylogenetic reconstruction

Dear Phylothusiasts, what is the most reliable way (implemented in R) to detect inversions within psbA-trnH in large datasets (>1 seq)? What kind of treatment would you suggest before attempting a phylogenetic reconstruction (except exclusion)? Best wishes, Andreas @moderator: feel free