[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

[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 -- Institute

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 liam.rev...@umb.edu wrote: On seeing this email, I also realized that to have

[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

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

mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo End of R-sig-phylo Digest, Vol 80, Issue 4 ** -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97

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

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 of the 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] 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