Class LikelihoodTool

Method Details

• 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

• optimiseUnrooted

  public static final Tree optimiseUnrooted(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.

  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

• optimiseClockConstrained

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

  Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted. The topology is unchanged.

  Parameters:

  tree - The tree with set branch lengths

  alignment - The alignment (sequence names must match tree)

  model - The substitution model to use

  optimiseModel - if true the model is optimised as well

  Returns:

  The resulting optimised tree

• optimiseSRDT

  public static final Tree optimiseSRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)

  Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter. This is equivalent to the TipDate model. The topology is unchanged.

  Parameters:

  tree - The tree with set branch lengths

  alignment - The alignment (sequence names must match tree)

  model - The substitution model to use

  tocd - The sample information object relating sequences to time or order

  optimiseModel - if true the model is optimised as well

  rateStore - storage space for the mutation rate, the initial value is used as the starting rate in the optimisation

  Returns:

  The resulting optimised tree

• optimiseMRDT

  public static final Tree optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)

  Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval. The topology is unchanged.

  Parameters:

  tree - The tree with set branch lengths

  alignment - The alignment (sequence names must match tree)

  model - The substitution model to use

  tocd - The sample information object relating sequences to time or order

  optimiseModel - if true the model is optimised as well

  rateStore - storage space for the mus, the initial values are used as the starting mus in the optimisation

  Returns:

  The resulting optimised tree

• optimiseMRDT

  public static final Tree optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore)

  Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals. The topology is unchanged.

  Parameters:

  tree - The tree with set branch lengths

  alignment - The alignment (sequence names must match tree)

  model - The substitution model to use

  tocd - The sample information object relating sequences to time or order

  optimiseModel - if true the model is optimised as well

  rateChangeTimes - the times (as related to the sample information) of when a new mu is used (should be of length mus.length -1 )

  rateStore - storage space for the mus, the initial values are used as the starting mus in the optimisation

  Returns:

  The resulting 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