Transfer Bootstrap

transferBootstrap assigns transfer bootstrap (Lemoine, Entfellner, Wilkinson, Correia, Felipe, De Oliveira, and Gascuel 2018) values to the (internal) edges.

Usage

transferBootstrap(tree, trees, phylo = TRUE, scale = TRUE)

Arguments

tree: The tree on which edges the bootstrap values are plotted.
trees: a list of trees (object of class "multiPhylo").
phylo: Logical, return a phylogentic tree with support value or a vector of bootstrap values.
scale: scale the values.

Value

a phylogentic tree (a phylo object) with bootstrap values assigned to the node labels.

References

Lemoine F, Entfellner JD, Wilkinson E, Correia D, Felipe MD, De Oliveira T, Gascuel O (2018). “Renewing Felsenstein’s phylogenetic bootstrap in the era of big data.” Nature, 556(7702), 452–456.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

fdir <- system.file("extdata/trees", package = "phangorn")
# RAxML best-known tree with bipartition support (from previous analysis)
raxml.tree <- read.tree(file.path(fdir,"RAxML_bipartitions.woodmouse"))
# RAxML bootstrap trees (from previous analysis)
raxml.bootstrap <- read.tree(file.path(fdir,"RAxML_bootstrap.woodmouse"))

tree_tbe <- transferBootstrap(raxml.tree,  raxml.bootstrap)
par(mfrow=c(1,2))
plotBS(tree_tbe)
# same as
plotBS(raxml.tree,  raxml.bootstrap, "p", "TBE")