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 tested this on MCC consensus trees
generated using Tree Annotator (from Beast software), which will also work with
your MrBayes outputs.
So you can do something like:
BayesPhy <- read.beast(“~/tree_MCC_TreeAnOut.nex”)
plot(BayesPhy) # optional arguments: cex=0.6, label.offset=0.5, no.margin=T,
root.edge=T, x.lim=c(-10,70), y.lim=c(-10,200))
node.support(BayesPhy$posterior, cutoff=0.95, digits=2, pos="pretty", col =
c("black"), cex=0.6)
node.support(BayesPhy$posterior, cutoff=0.95, mode="dots", col = c("black"),
cex=0.7)
# If its a timetree, you can add:
HPDbars(BayesPhy, label="height_95%_HPD", broken=T, lwd=3,
col=hsv(0.65,1,1,alpha=0.7))
data(gradstein04)
axisGeo(GTS = gradstein04, unit = c("epoch"), cex = 0.8, ages=FALSE, gridty=3,
gridcol="grey50")
axisPhylo(cex.axis=0.5, pos=-3, mgp=c(0,0.2,0))
text(0,0,labels="Ma", cex=0.5)
Hope that helps
—nate
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nathan S. Upham, Ph.D.
NSF Postdoctoral Associate
Yale University — Ecology and Evolutionary Biology
165 Prospect Street, New Haven, CT | 06511 | USA
http://jetzlab.yale.edu/ | http://vertlife.org/
Research Associate, Integrative Research Center (Mammals)
Field Museum of Natural History
1400 S. Lake Shore Drive, Chicago, IL | 60605 | USA
[email protected]<mailto:[email protected]> |
http://www.researchgate.net/profile/Nathan_Upham/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Aug 26, 2015, at 11:00 AM, Felipe Rossetto
<[email protected]<mailto:[email protected]>> wrote:
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(tree,p=0.95,check.labels = TRUE)
con<-consensus(tree,p=0.95,check.labels = TRUE)
plot(con)
I used redundant commands, but the consensus was plotted.
The problem is the consensus tree is unrooted, and I tried this command for
rooting it:
tree <- root(tree, "Bougainvillea_infesta") #Bougainvillea infesta is
outgroup
The problem I have three species of Bougainvillea as outgroup, and in the
consensus rooted (with one only species of Bougainvillea), Bougainvillea is
paraphyletic, and it is not true. I need force the monophyly of
Bougainvillea (as available in Beauti) but I didn't find the right command.
So, please, so someone know this commnad for root a tree with more than one
outgroup species, or root the tree with one outgroup species and then,
force the monophyly of the outgroup, if it has many species? Another
question is: is there a command which allows exporting the consensus with
the PP values?
Finally, I woud like to express my apologies to Vojtěch, please, forgive me!
Any problems, please, write me
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 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV:
https://urldefense.proofpoint.com/v2/url?u=http-3A__buscatextual.cnpq.br_buscatextual_visualizacv.do-3Fid-3DK4211230P7&d=AwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vIijt5ZvKOPcIOpF4No7UyIys6E9XUGVoE8kcxrgA6k&m=a7-LUMPqoqgIZakp38bP-VkRRvf5ep0e8373bfHqqLs&s=0MJ4-evw-nUes-tkfB4kxt2Dckx6O7WSkBpBA-PhSus&e=
2015-08-26 11:35 GMT-03:00 Felipe Rossetto
<[email protected]<mailto:[email protected]>>:
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 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV:
https://urldefense.proofpoint.com/v2/url?u=http-3A__buscatextual.cnpq.br_buscatextual_visualizacv.do-3Fid-3DK4211230P7&d=AwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vIijt5ZvKOPcIOpF4No7UyIys6E9XUGVoE8kcxrgA6k&m=a7-LUMPqoqgIZakp38bP-VkRRvf5ep0e8373bfHqqLs&s=0MJ4-evw-nUes-tkfB4kxt2Dckx6O7WSkBpBA-PhSus&e=
2015-08-26 11:16 GMT-03:00 Felipe Rossetto
<[email protected]<mailto:[email protected]>>:
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 root it with
only one species, the outgroup is paraphyletic and it is not true. So my
questions are: (1) Is here a command for forcing a monophyly of the
outgroup? (2) Is there a command for exporting this consesus tree with the
PP values?
Many thanks in advance
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 10.011
CEP: 86057-970
Londrina, Paraná, Brasil
CV:
https://urldefense.proofpoint.com/v2/url?u=http-3A__buscatextual.cnpq.br_buscatextual_visualizacv.do-3Fid-3DK4211230P7&d=AwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vIijt5ZvKOPcIOpF4No7UyIys6E9XUGVoE8kcxrgA6k&m=a7-LUMPqoqgIZakp38bP-VkRRvf5ep0e8373bfHqqLs&s=0MJ4-evw-nUes-tkfB4kxt2Dckx6O7WSkBpBA-PhSus&e=
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