Salut Catherine,
try this:
align1<-read.dna("datacr.fas", format="fasta") #class DNAbin
align2<- as.phyDat(align1) #class phyDat
treeMP <- pratchet(align2)
treeMP <- acctran(treeMP, align2) # add some edge.length
bs<-bootstrap.phyDat(align2, pratchet, bs=100) # 100 bootstraped MP trees
plotBS(midpoint(treeMP), bs, "phylogram")
add.scale.bar()
I hope this what you intended to do.
Regards,
Klaus
On Tue, Jun 3, 2014 at 9:32 AM, catherine reeb <[email protected]> wrote:
> Sorry I forgot the subject!
>
> "Boostrap on mp tree"
>
>
>
>
> 2014-06-03 9:14 GMT+02:00 catherine reeb <[email protected]>:
>
> > Hello,
> > I am trying to calcultae and plot bootstrap with pohangorn, but something
> > does not work :
> >
> > align1<-read.dna("datacr.fas", format="fasta") #class DNAbin
> > align2<- as.phyDat(align1) #class phyDat
> > treeMP <- pratchet(align2)
> > bs<-bootstrap.phyDat(treeMP.new, bs=100)#just for test
> >
> > but it gives
> > "Erreur dans rep(1:length(weight), weight) : argument 'times' incorrect"
> >
> >
> > thanks a lot!
> >
> >
> > --
> >
> > --
> >
> > Catherine Reeb
> > Museum National D'histoire Naturelle
> > Département Systématique et Evolution Case postale 39
> > UMR CNRS 7205
> >
> > 57 rue cuvier
> >
> > FRANCE-75005 Paris
> >
> > portable +33629375132
> > poste 0140793200
> >
> > [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > R-sig-phylo mailing list - [email protected]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
> > http://www.mail-archive.com/[email protected]/
> >
>
>
>
> --
>
> --
>
> Catherine Reeb
> Museum National D'histoire Naturelle
> Département Systématique et Evolution Case postale 39
> UMR CNRS 7205
>
> 57 rue cuvier
>
> FRANCE-75005 Paris
>
> portable +33629375132
> poste 0140793200
>
> [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-sig-phylo mailing list - [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/[email protected]/
>
--
Klaus Schliep
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - [email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/[email protected]/
