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.
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]