edu.rit.compbio.phyl

Class Upgma

java.lang.Object

edu.rit.compbio.phyl.Upgma

public class Upgma
extends java.lang.Object

Class Upgma provides the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm for phylogenetic tree construction. For further information, see:

• R. Sokal and C. Michener. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38:1409-1438, 1958.
• J. Felsenstein. Inferring Phylogenies. Sinauer Associates, 2004, pages 161-166.

Method Summary

Modifier and Type	Method and Description
static DnaSequenceTree	buildTree(DnaSequenceList seqList, Distance dcalc) Build a phylogenetic tree of the given DNA sequences.
static void	main(java.lang.String[] args) Main program.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Main program. Reads a DnaSequenceList from a file in interleaved PHYLIP format, constructs a phylogenetic tree using the UPGMA algorithm with Jukes-Cantor distances, prints the tree (including branch lengths) in Newick Standard format, and prints the squared error in the branch lengths as computed by the squaredError() method of class LeastSquaresBranchLengths.

Usage: java edu.rit.compbio.phyl.Upgma file
file = DNA sequence list file name

Throws:

java.lang.Exception

buildTree

public static DnaSequenceTree buildTree(DnaSequenceList seqList,
                                        Distance dcalc)

Build a phylogenetic tree of the given DNA sequences. The return value is a phylogenetic tree, including branch lengths, of the DNA sequences in seqlist, as constructed by the UPGMA algorithm. The DNA sequences in the tree are references to (not copies of) the DNA sequences in seqlist. The distances between the DNA sequences are calculated using the dcalc object.

Parameters:

seqList - List of DNA sequences.

dcalc - Object to calculate distances between DNA sequences.

Returns:

Phylogenetic tree.