optim.phylo.ls.all: Least squares phylogenetic estimation with an exhaustive...
In synDss: Recombination detection using synonymous distances

Description Usage Arguments Details Value Author(s) References

This function obtains the phylogeny which has the minimum value of the least squares criterion, among all possible phylogenies. An exhaustive search over all possible topologies is performed, to ensure that a global minimum is reached in the optimization routine.

1	optim.phylo.ls.all(D, set.neg.to.zero = TRUE, fixed = FALSE, tol = 1e-10, collapse = TRUE)

`D`	Distance matrix
`set.neg.to.zero`	logical; if TRUE, set negative values equal to 0.
`fixed`	logical; if TRUE, use a fixed topology for branch length estimation
`tol`	Tolerance
`collapse`	logical; if TRUE, then collapse branches with zero length

This function is a modification of optim.phylo.ls from phytools

An object of class "phylo" that is the least-squares tree with branch lengths; also returns the sum of squares in attr(tree,"Q-score").

Peter Chi

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217-223. doi:10.1111/j.2041-210X.2011.00169.x

synDss documentation built on May 2, 2019, 5:40 p.m.