Hye, This soltuion works well, but I cannot plot on the rooredt tree I built just before searching bootstrap. I saw that in the option "type", just "unrooted" was possible. The following code works,,but the tree is not rooted byt the group I gave. (i have also pb with node rotation, but it is another subject)
treeMP <- pratchet(align2) treeMP<-root(treeMP, "H_adunctus") treeMP<-acctran(treeMP, align2) nodelabels() treeMP.new<-rotate(treeMP,105 ) plot(treeMP.new, main="Parcimony", cex=0.4,label.offset=0.005) bs<- bootstrap.phyDat(align2, pratchet, bs=100) bs<- bootstrap.phyDat() plotBS(midpoint(treeMP), bs, type="phylogram",main="Parcimony bootstrap 100", cex=0.6, bscol="green") Thanks again 2014-06-03 9:43 GMT+02:00 Klaus Schliep <[email protected]>: > 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]/ > -- -- 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]]
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