Uses of Interface
pal.substmodel.SubstitutionModel

Silly idea stuff

recompute maximum-likelihood distances under new site pattern

update model of substitution

compute maximum-likelihood distances

initialisation

Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities

Calculate the likelihood given the conditional probabilites at the root

Extend the conditionals back in time by some distance, with some model

Create a Postriors object

Create a SimpleUnconstrainedLikelihoodModel instance

Optimise parameters to acheive maximum likelihood using an alternating stategy.

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.

Optimise parameters to acheive maximum likelihood using a combined stategy.

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.

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.

Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.

define model (a site pattern must have been set before calling this method)

Create a simple evaluator that uses UnrootedTreeSearch

A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.

Create an F84 model of substitution

Create a Jukes-cantor model of substitution

Create an neutral Yang Codon model (M1) of substitution

Create an Tamura-Nei model of substitution

A constructor (with no provided random number generator - a fresh one is created)

Inititalisation

Create a new Tree Searcher with a new sub tree attached

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

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

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

Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).