Hello, There is a program called "Path-O-Gen" (http://tree.bio.ed.ac.uk/software/pathogen/) which can (among other things) reroot a phylogeny with dated tips in the location most compatible with the assumption of a strict molecular clock, by using root-to-tip regression (Rambaut, Andrew. "Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies." Bioinformatics 16.4 (2000): 395-399.). I have written an R function which replicates this functionality (https://gist.github.com/rmcclosk/ea0fc1145cd086259ffc). I was wondering if there would be any interest in incorporating it into ape. I apologize in advance if a function to do this already exists, but I couldn't find one.
Thanks! -- Rosemary McCloskey Research Assistant BC Centre for Excellence in HIV/AIDS 608–1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6 email: [email protected] / [email protected] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
