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