Re: [R-sig-phylo] Extract all possible clades from a tree

de 8 (node 25) has 5 tips." >>>[1] "clade 9 (node 26) has 3 tips." >>>[1] "clade 10 (node 27) has 2 tips." >>>[1] "clade 11 (node 28) has 2 tips." >>>[1] "clade 12 (node 29) has 6 tips." >>>

Re: [R-sig-phylo] Extract all possible clades from a tree

f Michigan > Department of Ecology & Evolutionary Biology > Room 2071, Kraus Natural Sciences Building > Ann Arbor MI 48109-1079 > josep...@umich.edu <mailto:josep...@umich.edu> > > > >> On 5 Jan, 2017, at 15:50, Kamila Naxerova <knaxer...@partners.org >>

[R-sig-phylo] Extract all possible clades from a tree

Hi all, I would like to break a phylogenetic tree into all possible clades and then examine each one of them for certain characteristics. I am writing some code to do this from scratch, but it’s getting pretty cumbersome quickly. I was wondering whether there are some functions out there

Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo

to be placed interactively") > > You then click on the graphical window where you want to add the text. > > Best, > > Emmanuel > > Le 01/07/2016 05:47, Kamila Naxerova a �crit : >> Thanks so much for your reply, Liam. >> >> Most of the tip labels pl

Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo

Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 6/29/2016 5:11 PM, Kamila Naxerova wrote: >> Dear all, >> >> is there a way to adjust the positio

[R-sig-phylo] Adjust position of tip labels in plot.phylo

Dear all, is there a way to adjust the position of tip labels when plotted an unrooted tree with plot.phylo? Many thanks, Kamila The information in this e-mail is intended only for the ...{{dropped:11}} ___ R-sig-phylo mailing list -

[R-sig-phylo] Error in plotBS when number of taxa is small

Hi all, I am trying to attach bootstrap values to a small tree (just 4 taxa). plotBS() in the phangorn package gives me the following error: tree <- plotBS(phylotree,bstrees,type="phylogram",p=90) Error in if (drop[j]) next : missing value where TRUE/FALSE needed This error disappears and

[R-sig-phylo] Plotting rooted tree with bootstrap values (ape/phangorn)

Hi all, I have a (almost certainly trivial) question about plotting a rooted tree with bootstrap values using ape and phangorn. I am using a simple script that looks like this: dist <- daisy(matrix,metric="gower") nrooted <- root(nj(dist),outgroup=x) plot(nrooted) ## this plots the tree with