public final class TreeSearchTool
extends java.lang.Object
Title: TreeSearchTool
Description: An access point for a simple and stable interface to tree search methods
Constructor | Description |
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TreeSearchTool() |
Modifier and Type | Method | Description |
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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).
|
public Tree basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel)
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 treesm
- 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.public Tree basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
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 treesm
- 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 progresspublic Tree basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel)
a
- The related alignment, OTU labels must match that of the treesm
- 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.public Tree basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
a
- The related alignment, OTU labels must match that of the treesm
- 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 progresspublic static final Tree optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
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 treepublic static final Tree optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
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 treecallback
- An algorithm callback object for monitoring process of search algorithmpublic static final Tree optimiseClockConstrainedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
tree
- The tree (remains unchanged) - should be rootedalignment
- 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 treecallback
- An algorithm callback object for monitoring process of search algorithmpublic static final Alignment getMatchingDataType(Alignment alignment, SubstitutionModel model)
alignment
- The base alignmentmodel
- The substitution model that will be used with the alignment datapublic static final double calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
tree
- The tree with set branch lengthsalignment
- The alignment (sequence names must match tree)model
- The substitution model to use