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 availab
you might want to check out the Phybase package, it reads trees in a slightly
different way but I've had no problems reading in posterior trees from MrBayes
output. Like I said it's just a quick couple of command to convert from phybase
objects to ape objects
Cheers,
-Dan
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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):
install.packages('/home/dan/Downlo
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 speci
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 th
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 Univers
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 rand
Hi Kirston,
I generally convert DNAbin into general R objects like matrices, lists, and
vectors for my subsetting so I don't have to make DNAbin specific functions. I
typically use as.character() which converts DNAbin to matrix, then as.DNAbin()
which converts matrix back to DNAbin
example:
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 behalf of john d
Sent: Sunday, December