Hi Ross, What about Dendropy? It has several tree distances measures implemented, and can be easily scripted in Python (easy to use even without much knowledge of the language).
See http://pythonhosted.org/DendroPy/tutorial/treestats.html, section 3.3.10 at the bottom. HTH, Dan. -------------------------------------------------------- Daniel Fulop, Ph.D. Postdoctoral Scholar Dept. Plant Biology, UC Davis Maloof Lab, Rm. 2119 Life Sciences Addition, One Shields Ave. Davis, CA 95616 530-752-8086 dfu...@ucdavis.edu On Sep 21, 2013, at 3:00 AM, r-sig-phylo-requ...@r-project.org wrote: > Send R-sig-phylo mailing list submissions to > r-sig-phylo@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > or, via email, send a message with subject or body 'help' to > r-sig-phylo-requ...@r-project.org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > > 1. Re: Pairwise tree distance matrix (Ross Mounce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Sep 2013 11:25:47 +0100 > From: Ross Mounce <rcp...@bath.ac.uk> > To: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Pairwise tree distance matrix > Message-ID: <20130920112547.688b9dda2fb3288faaa34...@bath.ac.uk> > Content-Type: text/plain; charset=UTF-8 > > Hi Rob, > > Dave Bapst kindly brought this to my attention. > > I have a few suggestions for calculating pairwise RF distances between trees. > (Apologies if I don't exactly answer the original question) > > 1.) Firstly, I have to say, the very fastest solutions lie in implementations > currently outside of R e.g. > MrsRF. So if speed is vital I'd build a workflow around this, it's extremely > quick at all the all-to-all tree-to-tree calculations I've tried it with: > > * Matthews, S. and Williams, T. 2010. MrsRF: an efficient MapReduce algorithm > for analyzing large collections of evolutionary trees. BMC Bioinformatics > 11:S15-9. > > 2.) If you're looking for broad solutions (measuring tree distance with a > variety of measures, not just Robinson-Foulds) I'd recommend TreeCmp as that > does a wide variety of them: > > * Bogdanowicz, D., Giaro, K., and Wrobel, B. 2012. TreeCmp: Comparison of > trees in polynomial time. Evolutionary Bioinformatics pp. 475+. > > Sidenote: whilst being the computationally quickest and most commonly-used, > I'm sure both 'biologically' and in terms of discriminatory power > Robinson-Foulds is NOT the most optimal measure of tree-tree distance (but > hey, that won't stop people using it exclusively...). > > > 3.) I built a kludgy workflow myself from TNT -> R to better automate the > taxon-jackknifing tests first performed in: Cobbett, A., Wilkinson, M., and > Wills, M. 2007. Fossils impact as hard as living taxa in parsimony analyses > of morphology. Systematic biology 56:753-766. > > So if by chance you're doing these all-to-all tree distance calculations to > get at the mean-minimum tree distances between 2 different sets of trees you > might want to peruse my code which is here on github: > https://github.com/rossmounce/extinct_extant_chapter (see the diagram for a > visual explanation) > It's not the fastest or most elegant implementation possible... but it works. > (Apologies if this last option is not relevant to your use-case) > > > > Best, > > Ross > > > ---------- Forwarded message ---------- > From: Rob Lanfear <rob.lanf...@gmail.com> > Date: Thu, Sep 19, 2013 at 4:41 PM > Subject: [R-sig-phylo] Pairwise tree distance matrix > To: r-sig-phylo <r-sig-phylo@r-project.org> > > > Hi All, > > I'm looking for a method to calculate a pairwise distance matrix of RF > distances between a set of trees. > > Specifically, I know it's possible to do this in linear time (relative to > the number of taxa), using an algorithm proposed in 1985[1]. This algorithm > is implemented in various places (e.g. TreeSetVis in Mesquite), but I > couldn't find an implementation in R. > > If anyone knows of an implementation, or has ideas on where best to start > building one, please let me know. > > Cheers, > > Rob > > > [1] Day,W. H. E. 1985. Optimal algorithms for comparing trees with labeled > leaves. J. Classi?cation 2:7?28. > > -- > Rob Lanfear > Research Fellow, > Ecology, Evolution, and Genetics, > Research School of Biology, > Australian National University > > > > -- > -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- > Ross Mounce > PhD Student (writing-up now!) > Fossils, Phylogeny and Macroevolution Research Group > University of Bath, 4 South Building, Lab 1.07 > Systematics Association Council Member > http://about.me/rossmounce > > > > ------------------------------ > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > End of R-sig-phylo Digest, Vol 68, Issue 14 > ******************************************* [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
