[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

[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]]

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

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: