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

2017-02-03 Thread Joe Felsenstein
Emmanuel wrote: > > There is no distance formula for HKY or GTR model. For GTR, Rodrı́guez et > al. developed a procedure to calculate a distance (also in Yang's 2006 > book). An example is given below with the woodmouse: > > matlog <- function(x) { > tmp <- eigen(X) > V <- tmp$vectors >

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

2017-02-03 Thread Emmanuel Paradis
Dear Andreas, There is no distance formula for HKY or GTR model. For GTR, Rodrı́guez et al. developed a procedure to calculate a distance (also in Yang's 2006 book). An example is given below with the woodmouse: matlog <- function(x) { tmp <- eigen(X) V <- tmp$vectors U <-

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

2017-02-02 Thread Jacob Berv
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

2017-02-02 Thread kolte...@rub.de
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