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java.lang.Objectpal.treesearch.TreeSearchTool
public final class TreeSearchTool
Title: TreeSearchTool
Description: An access point for a simple and stable interface to tree search methods
Constructor Summary | |
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TreeSearchTool()
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Method Summary | |
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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). |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public TreeSearchTool()
Method Detail |
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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 progress
public 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 progress
public 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 tree
public 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 algorithm
public 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 algorithm
public static final Alignment getMatchingDataType(Alignment alignment, SubstitutionModel model)
alignment
- The base alignmentmodel
- The substitution model that will be used with the alignment data
public 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
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