Thank you François,
I was trying to use consensus() from ape, but when I try to write a nexus
file I get an error message:
> trees<-read.nexus("1000_trees.nex")
> consensus(trees,p=1,check.labels=TRUE)
> write.nexus(my_tree,"consensus_birds.nex")
#NEXUS
[R-package APE, Wed Jul 15 14:49:14 2015]
BEGIN TAXA;
DIMENSIONS NTAX = 59;
TAXLABELS
Rhynchotus_rufescens
Apteryx_haastii
Dromaius_novaehollandiae
(...)
;
END;
BEGIN TREES;
TRANSLATE
Error in y$tip.label : $ operator is invalid for atomic vectors
My only problem now is to create the file. I'm going to try the softwares
you pointed.
Best regards,
Sérgio.
ᐧ
2015-07-15 14:49 GMT+01:00 François Michonneau <
[email protected]>:
> Hi Sergio,
>
> Not in R, but you can use PAUP, MrBayes or Dendropy (my recommendation).
>
> Cheers,
> -- François
>
> 2015-07-15 7:53 GMT-04:00 Sergio Ferreira Cardoso
> <[email protected]>:
> > Dear all,
> >
> > I have a nexus file with 1000 trees on it with divergence times as branch
> > lengths. Does anyone know about a package that can make a consensus tree
> > out of my 1000 trees?
> > Thanks in advance.
> >
> > Best regards,
> > Sérgio.
> >
> > --
> > Com os melhores cumprimentos,
> > Sérgio Ferreira Cardoso.
> >
> > --------------------
> >
> > Best regards,
> > Sérgio Ferreira Cardoso
> >
> >
> >
> >
> > MSc. Paleontology candidate
> > Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa
> > Geociências - Universidade de Évora
> >
> > Lisboa, Portugal
> >
> > [[alternative HTML version deleted]]
> >
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--
Com os melhores cumprimentos,
Sérgio Ferreira Cardoso.
--------------------
Best regards,
Sérgio Ferreira Cardoso
MSc. Paleontology candidate
Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa
Geociências - Universidade de Évora
Lisboa, Portugal
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