distory (version 1.4.1)

distory-package: Distance Between Phylogenetic Histories

Description

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.

Details

A description of the algorithm used for the distance computation can be found in help(dist.multiPhylo).

References

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.

Examples

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))