Description Details Author(s) References Examples

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).

John Chakerian <[email protected]> and Susan Holmes <[email protected]>

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))
``` |

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