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,
- Christie
On Wed, Aug 26, 2015 at 10:00 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: http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
>
>
> 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:
> http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
> >
> >
> > 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:
> http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4211230P7
> >>
> >>
> >
>
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>
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