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("Bougainvillea_infesta", "Bougainvillea_spectabilis",
"Bougainvillea_glabra")
for (i in 1:length(tree)) # ''force monophyly of the outgroup, if i do not
use these command, outgroup turn a praphyletic grade
tree[[i]] <- root(tree[[i]], outgr, resolve.root = TRUE)
consensus(tree,p=0.5,check.labels = TRUE)
con<-consensus(tree,p=0.5,check.labels = TRUE)
plotBS(con, tree, "phylogram") -> con.l # plot the PP or bs values in the
rooted consensus
write.tree(con.l, file="c.tre")
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: http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
2015-08-26 15:37 GMT-03:00 Upham, Nathan <[email protected]>:
> 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] | http://www.researchgate.net/profile/Nathan_Upham/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> On Aug 26, 2015, at 11:00 AM, Felipe Rossetto <[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]>:
>
> 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]>:
>
> 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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