getTree: Build phylogenies from multiple gene data

Description

This function builds separate phylogenetic trees for each gene in a multidna object, specifying a method for computing pairwise distances between individuals, and a method to build the tree from the distance matrix. By default, procedures from ape are used.

Usage

getTree(x, pool = FALSE, genes = TRUE, model = "N",
  pairwise.deletion = TRUE, method = nj, ladderize = TRUE,
  negative.branch.length = FALSE, ...)

Value

a multiPhylo object

Arguments

x: a multidna object.
pool: a logical indicating if all genes should be pooled (concatenated) to obtain a single tree; defaults to FALSE.
genes: an optional vector indicating the genes to retain for the concatenation; any way to subset the list in x@dna is acceptable; by default, all genes are used.
model: a character string passed to dist.dna describing the model to be used to compute genetic distances; defaults to 'N', the absolute number of mutations separating sequences.
pairwise.deletion: a logical passed to dist.dna indicating if pairwise deletions should be used; the alternative is to remove all sites for which at least one missing value is present.
method: a function building a tree from a matrix of pairwise genetic distances.
ladderize: a logical indicating if the tree should be ladderized; defaults to TRUE.
negative.branch.length: a logical indicating if negative branch lengths should be allowed (e.g. in the case of Neighbor-Joining reconstruction), or not, in which case they are set to 0 (FALSE, default).
...: further arguments passed to the tree reconstruction method defined by 'method'.

Author

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

Run this code


## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
plot(x)

## make trees, default parameters
trees <- getTree(x)
trees
plot(trees, type="unrooted")

## make one single tree based on concatenated genes
tree <- getTree(x, pool=TRUE)
tree
plot(tree, type="unrooted")