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 t
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 miss
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
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
comm.p
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)
d<-sapp
Yes, it looks like it! Thank you! Guess I was making it more complicated
than it needed to be.
Cheers,
Zach
On Thu, Feb 2, 2017 at 2:36 PM, Liam J. Revell wrote:
> Hi Zach.
>
> Do you just mean the mean patristic distance among all pairwise
> combinations of species in each assemblage?
>
> If