Dear Andreas,
you could play around with dist.ml() in phangorn. It does ML distances
optimisation and you can supply a rate matrix and base frequencies for all
the distances. However this is of course slower than the closed form
solutions, but it can handle ambiguous states nicely. I can make a lit
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$vectors
>
Dear Andreas,
There is no distance formula for HKY or GTR model. For GTR, Rodrı́guez
et al. developed a procedure to calculate a distance (also in Yang's
2006 book). An example is given below with the woodmouse:
matlog <- function(x) {
tmp <- eigen(X)
V <- tmp$vectors
U <- diag(lo
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
> implementation of HKY and GTR dista
