pal.treesearch

Class TreeSearchTool

java.lang.Object

pal.treesearch.TreeSearchTool

public final class TreeSearchTool
extends java.lang.Object

Title: TreeSearchTool

Description: An access point for a simple and stable interface to tree search methods

Version:

1.0

Author:

Matthew Goode

Constructor Summary

Constructors

Constructor and Description
TreeSearchTool()

Method Summary

Methods

Modifier and Type	Method and Description
Tree	basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel) Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
Tree	basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback) Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
Tree	basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel) Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
Tree	basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback) Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
static double	calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model) Calculate the log likelihood of a particular set of phylogenetic data
static Alignment	getMatchingDataType(Alignment alignment, SubstitutionModel model) Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)
static Tree	optimiseClockConstrainedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback) Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.
static Tree	optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel) Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
static Tree	optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback) Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).

Methods inherited from class java.lang.Object

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

Constructor Detail

TreeSearchTool

public TreeSearchTool()

Method Detail

basicUnrootedTreeMLSearch

public Tree basicUnrootedTreeMLSearch(Tree baseTree,
                             Alignment a,
                             SubstitutionModel sm,
                             boolean optimiseModel)

Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree

Parameters:

baseTree - The starting tree (which may or may not be unrooted - will be unrooted)

a - The related alignment, OTU labels must match that of the tree

sm - The related substitution model. The data type of the model should match that of the alignment. The parameters of this model may change if the optimise model is choosen.

optimiseModel - If true the substitution model will be optimised concurrently with the tree. This will change in the input model.

Returns:

The optimised tree (the original tree is *not* altered)

basicUnrootedTreeMLSearch

public Tree basicUnrootedTreeMLSearch(Tree baseTree,
                             Alignment a,
                             SubstitutionModel sm,
                             boolean optimiseModel,
                             AlgorithmCallback callback)

Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree

Parameters:

baseTree - The starting tree (which may or may not be unrooted - will be unrooted)

a - The related alignment, OTU labels must match that of the tree

sm - The related substitution model. The data type of the model should match that of the alignment. The parameters of this model may change if the optimise model is choosen.

optimiseModel - If true the substitution model will be optimised concurrently with the tree. This will change in the input model.

callback - An AlgorithmCallback object used to control and monitor the search progress

Returns:

The optimised tree (the original tree is *not* altered)

basicUnrootedTreeMLSearch

public Tree basicUnrootedTreeMLSearch(Alignment a,
                             SubstitutionModel sm,
                             boolean optimiseModel)

Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree

Parameters:

a - The related alignment, OTU labels must match that of the tree

sm - The related substitution model. The data type of the model should match that of the alignment. The parameters of this model may change if the optimise model is choosen.

optimiseModel - If true the substitution model will be optimised concurrently with the tree. This will change in the input model.

Returns:

The optimised tree

basicUnrootedTreeMLSearch

public Tree basicUnrootedTreeMLSearch(Alignment a,
                             SubstitutionModel sm,
                             boolean optimiseModel,
                             AlgorithmCallback callback)

Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree

Parameters:

a - The related alignment, OTU labels must match that of the tree

sm - The related substitution model. The data type of the model should match that of the alignment. The parameters of this model may change if the optimise model is choosen.

optimiseModel - If true the substitution model will be optimised concurrently with the tree. This will change in the input model.

callback - An AlgorithmCallback object used to control and monitor the search progress

Returns:

The optimised tree

optimiseUnrootedFixed

public static final Tree optimiseUnrootedFixed(Tree tree,
                         Alignment alignment,
                         SubstitutionModel model,
                         boolean optimiseModel)

Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree). The topology is unchanged. No topology changes are made!

Parameters:

tree - The tree (remains unchanged)

alignment - The alignment (sequence names must match tree)

model - The substitution model to use (is changed if optimisation of the model is choosen)

optimiseModel - if true the model is also optimised, otherwise just the tree

Returns:

The optimised tree

optimiseUnrootedFixed

public static final Tree optimiseUnrootedFixed(Tree tree,
                         Alignment alignment,
                         SubstitutionModel model,
                         boolean optimiseModel,
                         AlgorithmCallback callback)

Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree). The topology is unchanged. No topology changes are made!

Parameters:

tree - The tree (remains unchanged)

alignment - The alignment (sequence names must match tree)

model - The substitution model to use (is changed if optimisation of the model is choosen)

optimiseModel - if true the model is also optimised, otherwise just the tree

callback - An algorithm callback object for monitoring process of search algorithm

Returns:

The optimised tree

optimiseClockConstrainedFixed

public static final Tree optimiseClockConstrainedFixed(Tree tree,
                                 Alignment alignment,
                                 SubstitutionModel model,
                                 boolean optimiseModel,
                                 AlgorithmCallback callback)

Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point. The topology is unchanged -no topology changes are made!

Parameters:

tree - The tree (remains unchanged) - should be rooted

alignment - The alignment (sequence names must match tree)

model - The substitution model to use (is changed if optimisation of the model is choosen)

optimiseModel - if true the model is also optimised, otherwise just the tree

callback - An algorithm callback object for monitoring process of search algorithm

Returns:

The optimised tree

getMatchingDataType

public static final Alignment getMatchingDataType(Alignment alignment,
                            SubstitutionModel model)

Creates a new alignment that has a compatible data type with a substution model (needed for likelihood stuff)

Parameters:

alignment - The base alignment

model - The substitution model that will be used with the alignment data

Returns:

An appropriately converted alignment

calculateLogLikelihood

public static final double calculateLogLikelihood(Tree tree,
                            Alignment alignment,
                            SubstitutionModel model)

Calculate the log likelihood of a particular set of phylogenetic data

Parameters:

tree - The tree with set branch lengths

alignment - The alignment (sequence names must match tree)

model - The substitution model to use

Returns:

The log likelihood