[R-sig-phylo] PGLS, polytomies, degrees of freedom and multiple specimens
Dear all, Can somebody tell whether one should subtract degrees of freedom when applying PGLS with a phylogeny containing soft polytomies? And does it make a difference if polytomies originate from data from multiple specimens of species? cheers, Popko Wiersma - I reposted this message because the first attempt did not show the text directly in the message body. Apologies for any confusion - ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Multiple sequence alignment in R?
Hello, Is clustal multiple sequence alignment implemented in any R packages, or is there an easy way to call ClustalW on your hard drive from R, perhaps with system() Sincerely, Scott Chamberlain Rice University, EEB Dept. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] PGLS, polytomies, degrees of freedom and multiple specimens
Hi Popko, My sense is that if the polytomy is hard, it is never necessary to subtract a degree of freedom. If the polytomy is firm (sensu Purvis Garland 1993) - in that the true tree is fully bifurcating but we cannot resolve a multifurcating node due primarily to rapid divergence of the descendant taxa - then subtracting a degree of freedom will probably be excessively conservative. If the polytomy is truly soft (sensu Maddison 1989; Garland Diaz-Uriarte 1999), then subtracting a degree of freedom for each extra furc will probably also be conservative. [As Rohlf 2001 points out, this would imply zero degrees of freedom if the phylogeny was completely unresolved (p. 2154), which seems excessive.] Some of these issues are discussed in Garland Diaz-Uriarte (1999; Syst. Biol.) and elsewhere. I'm sure that other subscribers to the list could add significant insight to this issue beyond what I am able to offer. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://www.bio.umb.edu/facstaff/faculty_Revell.html (new) email: liam.rev...@umb.edu (new) blog: http://phytools.blogspot.com On 2/22/2011 5:31 AM, Popko Wiersma wrote: Dear all, Can somebody tell whether one should subtract degrees of freedom when applying PGLS with a phylogeny containing soft polytomies? And does it make a difference if polytomies originate from data from multiple specimens of species? cheers, Popko Wiersma - I reposted this message because the first attempt did not show the text directly in the message body. Apologies for any confusion - ___ 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
Re: [R-sig-phylo] Multiple sequence alignment in R?
You can call any command-line thing from R with system(). Typically I use R to write the control file (e.g. for r8s), then do something like... cmdstr = paste(program_name, -options, control_file, output.log, sep= ) system(cmdstr) Cheers! Nick On 2/22/11 5:42 AM, Scott Chamberlain wrote: Hello, Is clustal multiple sequence alignment implemented in any R packages, or is there an easy way to call ClustalW on your hard drive from R, perhaps with system() Sincerely, Scott Chamberlain Rice University, EEB Dept. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Evolution http://ib.berkeley.edu/courses/ib200b/ http://phylo.wikidot.com/ Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: mat...@berkeley.edu Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 - [W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together. Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer, 14(1), 35-44. Fall 1989. http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
