phylonet.coalescent
Class GeneTreeRefinement

java.lang.Object
  phylonet.coalescent.GeneTreeRefinement

public class GeneTreeRefinement
extends java.lang.Object

This class refines and roots gene trees with respect to a given rooted binary species tree "Algorithms for MDC-based multi-locus phylogeny inference." RECOMB 2011

Author:

Yun

Constructor Summary

GeneTreeRefinement()

Method Summary

static void	main(java.lang.String[] args)
static void	printUsage() Print the help information of the command format
static void	processGeneTrees(java.util.List<Tree> gts, Tree st, java.util.Map<java.lang.String,java.util.List<java.lang.String>> species2alleles, boolean rooted, double bootstrap, java.lang.String path) Refine and root a set of gene trees optimally with respect to a given species tree
static void	refineRootedGeneTrees(java.util.List<Tree> gts, Tree st, java.util.HashSet<STITreeCluster> speciesClusters) Refine a set of rooted gene trees with respect to a species tree
static void	rootGeneTrees(java.util.List<Tree> gts, Tree st) Root a set of unrooted gene trees with respect to a species tree

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneTreeRefinement

public GeneTreeRefinement()

Method Detail

main

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

printUsage

public static void printUsage()

Print the help information of the command format

processGeneTrees

public static void processGeneTrees(java.util.List<Tree> gts,
                                    Tree st,
                                    java.util.Map<java.lang.String,java.util.List<java.lang.String>> species2alleles,
                                    boolean rooted,
                                    double bootstrap,
                                    java.lang.String path)

Refine and root a set of gene trees optimally with respect to a given species tree

Parameters:

gts - a list of given gene trees

st - a given species tree

taxonMap - Maps gene tree taxa to species tree taxa.

rooted - whether treating the gene trees and species tree rooted or not

refineRootedGeneTrees

public static void refineRootedGeneTrees(java.util.List<Tree> gts,
                                         Tree st,
                                         java.util.HashSet<STITreeCluster> speciesClusters)

Refine a set of rooted gene trees with respect to a species tree

Parameters:

gts - a set of gene trees

st - a given species tree

rootGeneTrees

public static void rootGeneTrees(java.util.List<Tree> gts,
                                 Tree st)

Root a set of unrooted gene trees with respect to a species tree

Parameters:

gts - a set of gene trees

st - a given species tree