| klastorin {ape} | R Documentation |
The function klastorin uses the method by Klastorin's (1982) as
suggested by Misawa and Tajima (2000) for identifying groups within
gene trees.
klastorin(phy)
phy |
a phylogenetic tree, i.e. an object of class "phy". The root of the tree should make
sense biologically.
|
A vector indication the class affiliation for each sequence/taxon in the tree.
Gangolf Jobb (http://www.treefinder.de)
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.
# 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]