Greetings all,
I am building some R simulations to assess patterns of different demographic
histories in simulated phylogenies which has me keeping track of a large number
of summary statistics for simulated gene trees and species trees. Over all I
have been very happy with the programs
Hi Melisa,
I agree with Brian, so far I have used phybase to do this.
I haven't tested it completely but I believe you can use the getcoaltime()
command from phybase to get at this information. You can try this code (most of
which is from the phybase manual):
Hi Marcelo,
I'm not familiar with that specific function in Mesquite but from the
explanation I saw on the Mesquite website you may want to check out the package
phybase by Liang Liu (http://code.google.com/p/phybase/). It has functions to
simulate coalescent trees or DNA sequences from a
Apologies for not replying to the list correctly the first time!
Hi Fabricia,
This may look a little complicated but it's pretty easy to get any string of
characters into a matrix using the s2c function in seqinr and from there it's
simple to get them into ape's DNAbin by running the matrix
Hi Imran,
I'm by no means an expert on phylogenetic signal with incomplete phylogenies
but I would check out the GEIGER package, specifically the mecca function. I
think mecca is set up to do estimates based on incomplete tip sampling.
Cheers,
-Dan Gates
PhD candidate
Smith/Pilson Lab
Hi Romain,
I think I've done something similar to this by searching the subtrees for the
name of the taxa in question. The code is probably pretty slow on really big
trees (since the subtrees function takes a while).
library(phybase)
library(phytools)
set.seed(5)
#make 100 20 tip trees
Hi Carlos,
I would check out phybase at
http://faculty.franklin.uga.edu/lliu/content/phybase . I have used it to
simulate gene trees from species trees. It works quite well and is very fast.
-Dan
From: R-sig-phylo on