I'm trying to make a consensus tree from the MrBayes.t file output, and I
used the following comands for this:
library(ape)
library(geiger)
library(phangorn)
read.nexus("infile.nex.run1.t", tree.names =NULL)#read the .t file (7500
trees)
tree<-read.nexus("infile.nex.run1.t")
outgr <- c("Bougainvil
Many thanks Nathan and Christie!
The monophyly of the outgroup was ''forced'' due to a command that Emmanuel
sent me (in yellow):
library(ape)
library(geiger)
library(phangorn)
read.nexus("infile.nex.run1.t", tree.names =NULL)
tree<-read.nexus("infile.nex.run1.t")
outgr <- c("Bougainvillea_infesta
Hi Felipe
I would try the "read.beast()” function in the phyloch package, which you can
download here (I don’t think it is on CRAN):
http://www.christophheibl.de/Rpackages.html
The function should store the PP values as a variable in the tree object when
you load the file— however, I have only
Hi Felipe,
The root command supports setting more than one species as the outgroup.
All you have to do is give it a vector of all the species you want to use.
So, it would look something like tree <- root(tree,
c("Bougainvillea_infesta", "Bougainvillea_sp2", "Bougainvillea_sp3"))
Hope this works,
Maybe I did not explain well my difficult, I inserted the .t file generated
by MrBayes with the 25% of the trees discarded in R. Then I tried, in R, to
creat a consensus tree using these commands:
read.nexus("infile.nex.run1.t", tree.names =NULL)
tree<-read.nexus("infile.nex.run1.t")
consensus(tre
OK, then, please, write also commands You used. It helps to help... Generally,
for first question I'm not sure, but for the second, write.tree() writes all
data presented in respective phylo object. So yes. And, please, if I may ask
You, 1) answer to the list (not personally) and 2) usage of ton
Someone thought I having difficulties in MrBayes, but the point I need help
is in R and not in MrBayes
Thanks
Felipe Rossetto
Herbário FUEL
Departamento de Biologia Animal e Vegetal
Universidade Estadual de Londrina
Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
Caixa postal 10.
Hello,
I might be missing some point, but this forum is about R & phylogeny. If You
have problems with MrBayes, it'd probably be better to ask somewhere else.
Seqanswers.com and/or MrBayes' homepage could be good point in this case...
Sincerely,
Vojtěch
26. srpna 2015 16:16:14 CEST, Felipe Ross
Hi there,
I'm using R for creating a consensus tree of non discarded burn-in trees,
and I used the MrBayes .t file for it. But The consensus is unrooted, and I
have 3 species as outgroup, and I'm not having sucess in root the tree with
these 3 outgroups (species from the same genus), and when I roo
