ape (version 1.8-2)

klastorin: Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)

Description

The function klastorin uses the method by Klastorin's (1982) as suggested by Misawa and Tajima (2000) for identifying groups within gene trees.

Usage

klastorin(phy)

Arguments

phy

a phylogenetic tree, i.e. an object of class "phy". The root of the tree should make sense biologically.

Value

• A vector indication the class affiliation for each sequence/taxon in the tree.

References

Klastorin T.D. (1982) An alternative method for hospital partition determination using hierarchical cluster analysis. Operations Research 30,1134--1147.

Misawa, K. (2000) A simple method for classifying genes and a bootstrap test for classifications. Molecular Biology and Evolution, 17, 1879--1884.

See Also

opsin.

Examples

library(ape)

# find groups in landplant tree
data("landplants.newick")
tree1 <- read.tree(text = landplants.newick)
plot(tree1, label.offset = 0.001)
klastorin(tree1)
tree1$tip.label

# find groups in opsin tree
data("opsin.newick")
tree2 <- read.tree(text = opsin.newick)
plot(tree2,label.offset = 0.01)
groups <- klastorin(tree2)
groups
tree2$tip.label[groups==1]
tree2$tip.label[groups==2]
tree2$tip.label[groups==3]
tree2$tip.label[groups==4]
tree2$tip.label[groups==5]