The 'distory' package provides functions for computing geodesic distances between phylogenetic trees, as well as functions which use this distance. Methods for computing Gromov delta-hyperbolicity, Markov Chain Monte Carlo routines in tree space, and per-position leverage for DNA sequences are included.
A description of the algorithm used for the distance computation can be found in help(dist.multiPhylo).
Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.
Billera, L. J., Holmes, S. P., and Vogtmann, K. (2001) Geometry of the space of phylogenetic trees. _Adv. Appl. Math_, *27*, 733-767.
Megan Owen, J. Scott Provan, "A Fast Algorithm for Computing Geodesic Distances in Tree Space," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 Jan. 2010.
1 2 3 4 5 6 7 8 9 10 11 12 13
data(woodmouse) otree <- root(nj(dist.dna(woodmouse)), "No305", resolve.root=TRUE) breps = 250 trees <- boot.phylo(otree, woodmouse, B=breps, function(x) root(nj(dist.dna(x)), "No305", resolve.root=TRUE),trees=TRUE) combined.trees <- c(list(otree), trees$trees) tree.dists <- dist.multiPhylo(combined.trees) mdres <- cmdscale(tree.dists, k=breps, add=TRUE) plot(mdres$points[,1], mdres$points[,2], col = c("red", rep("black", breps))) text(mdres$points[,1], mdres$points[,2], labels=1:(breps+1), cex=0.7, adj=c(0,2))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.