edu.rit.compbio.phyl

Class PhylogenyParsBnbSeq

java.lang.Object

edu.rit.compbio.phyl.PhylogenyParsBnbSeq

public class PhylogenyParsBnbSeq
extends java.lang.Object

Class PhylogenyParsBnbSeq is a sequential program for maximum parsimony phylogenetic tree construction using branch-and-bound search. The program reads a DnaSequenceList from a file in interleaved PHYLIP format, constructs a list of one or more maximum parsimony phylogenetic trees using branch-and-bound search, and stores the results in an output directory. If the third command line argument N is specified, only the first N DNA sequences in the file are used; if N is not specified, all DNA sequences in the file are used. If the fourth command line argument T is specified, the program will only report the first T maximum parsimony phylogenetic trees it finds; if T is not specified, the default is T = 100.

To examine the results, use a web browser to look at the "index.html" file in the output directory. For further information, see class Results.

Usage: java edu.rit.compbio.phyl.PhylogenyParsBnbSeq infile outdir [ N [ T ] ]
infile = Input DNA sequence list file name
outdir = Output directory name
N = Number of DNA sequences to use (default: all)
T = Number of trees to report (default: 100)

Method Summary

Modifier and Type	Method and Description
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.

Throws:

java.lang.Exception