[R-sig-phylo] Is my subset of species random?

, in other cases they may be preferably in some clades. Does any measure of this kind exist (ideally implemented in R)? Best wishes, Ondrej Mikula -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic

[R-sig-phylo] mulRF distance

Dear colleagues, is anybody aware of any R implementation of mulRF distance introduced by Chaudhary et al. 2013 & 2014? Best regards, Ondrej -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Insti

[R-sig-phylo] how to add phylogenetic tree to an existing plot

me metadata and with such argument it would become as easy as to overlay it. Best wishes, Ondřej -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences o

Re: [R-sig-phylo] R-sig-phylo Digest, Vol 80, Issue 4

(972)-8-6360-134 > holz...@post.tau.ac.il > http://iui-eilat.ac.il/People/AcademicStaffProfile.aspx?sid=106 > > > > > > [[alternative HTML version deleted]] > > > > -- > > ___ > R

[R-sig-phylo] phyloxml

Dear all, are you aware of any routine importing phylogenetic trees in .phyloxml format into R? Best wishes, Ondřej -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Acad

Re: [R-sig-phylo] basal dichotomy in phylo object

Dear Liam and Klaus, thanks a lot for your suggestions. "174" and "500" are actually labels of the nodes, but I used their numbers instead and it works well. All the best Ondrej On 25 October 2011 17:28, Liam J. Revell wrote: > On seeing this email, I also realized that to have node numbers up

[R-sig-phylo] basal dichotomy in phylo object

Hello, I have an unrooted tree, but I know that basal dichotomy is between nodes labeled "174" and "500". I am wandering how to indicate it in the object of class 'phylo'. I tried 'root' function of 'ape' but with no success. I will be grateful for any advice. Best wishes Ondrej Mikula -- Institu

Re: [R-sig-phylo] squared-change parsimony reconstruction

The problem with function ace is that it is designed for univariate data (if I understand the help file well). Moreover I would like to take variability in branch lengths into account. So I´m looking for a function doing weighted squared-change parsimony on multivariate data, but perhaps it is some

[R-sig-phylo] squared-change parsimony reconstruction

Dear all, I would like to make squared-change parsimony reconstruction of ancestral states for continuous multivariate data as recommended by: Rohlf, F. J. 2002. Geometric morphometrics in phylogeny. Pp. 175-193 in Forey, P. and N. Macleod (eds.) Morphology, shape and phylogenetics. Francis & Tayl