edu.rit.compbio.phyl
Class PhylogenyParsBnbHyb

java.lang.Object
  edu.rit.compbio.phyl.PhylogenyParsBnbHyb

public class PhylogenyParsBnbHyb
extends Object

Class PhylogenyParsBnbHyb is a hybrid parallel 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 [ -Dpj.np=Kp ] [ -Dpj.nt=Kt ] [ -Dpj.schedule=schedule ] edu.rit.compbio.phyl.PhylogenyParsBnbHyb infile outdir [ N [ T ] ]
Kp = Number of parallel processes (default: 1)
Kt = Number of parallel threads per process (default: number of CPUs)
schedule = Load balancing schedule (default: dynamic(1))
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

static void

main(String[] args) Main program.

Methods inherited from class java.lang.Object

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

Method Detail

main

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

Main program.

Throws:

Exception