I have not tried this, but why should you need to set the branch lengths equal to one? That is not a requirement of the squared-change parsimony algorithm (or ML equivalent) per se. (With variable branch lengths, people often refer to it as weighted squared-change parsimony.) Maybe this is just a limitation in ACE?
Also, how does ACE handle polytomies? I know that some algorithms have trouble with polytomies, which may be indicated as zero-length branches. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Sam Brown [s_d_j_br...@hotmail.com] Sent: Friday, August 26, 2011 5:11 PM To: r-sig-phylo@r-project.org; onmik...@gmail.com Subject: Re: [R-sig-phylo] squared-change parsimony reconstruction >> Date: Thu, 25 Aug 2011 13:13:47 +0200 >> From: Ond?ej Mikula <onmik...@gmail.com> >> To: r-sig-phylo@r-project.org >> Subject: [R-sig-phylo] squared-change parsimony reconstruction >> Message-ID: >> <CAPJtSLMXJ8y=rHguP4eqEKOqcEuxvYGSjGsg+D=jmq8w6sb...@mail.gmail.com> >> Content-Type: text/plain >> >> Dear all, >> >> I would like to make squared-change parsimony reconstruction of ancestral >> states for continuous multivariate data as recommended by: Hi Ondrej This can be done by setting the branch lengths of your tree to '1' and running ace(vector_of_states, your_tree, type = "continuous", method = "ML") See also the R-phylo wiki: http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction Cheers! Samuel Brown [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
