forester v1.2

forester.tools
Class Root

java.lang.Object
  |
  +--forester.tools.Root

public class Root
extends java.lang.Object

Version:
0.91 -- last modified: 07/17/00
Author:
Christian M. Zmasek

Constructor Summary
Root()
           
 
Method Summary
static Tree[] findRoot(Tree gene, Tree species)
          The purpose of this method is to root a gene tree by minimizing the number of duplications when compared to a species tree.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Root

public Root()
Method Detail

findRoot

public static Tree[] findRoot(Tree gene,
                              Tree species)
                       throws java.lang.Exception
The purpose of this method is to root a gene tree by minimizing the number of duplications when compared to a species tree. Returns an array of rooted Trees which have the minimal number of duplications. The most parsimonious sequence of speciation and duplication events is assumed. Tree species is a species Tree to which the gene Tree gene is compared to. Precondiations: Both Trees must be completely binary. The species Tree must be rooted. Species found in gene Tree must be a subset of those found in species Tree. Both Trees must have species names in the species name field of their Nodes. (See "TreeHelper.cleanSpeciesNamesInExtNodes" and and "TreeHelper.extractSpeciesNameFromSPseqName".)
Parameters:
gene - a gene Tree
specie - a species Tree
Returns:
array of rooted Trees which have the minimal number of duplications

forester v1.2