Uses of Interface
pal.tree.Tree

Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).

extracts intervals from clock tree.

extracts intervals from serial clock tree.

take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.

Silly idea stuff

Returns the (parameterized) tree of this likelihood value.

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.

Calculate the log likelihood of a particular set of phylogenetic data

Optimise model parameters only 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, over general time intervals.

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

define tree ,(must only be called only after a site pattern has been defined).

Constructor taking site pattern, tree and model.

Constructor taking site pattern, tree rate matrix, and a rate distribution

may be implemented by sub classes

constructs an SUPGMA tree from pairwise distances.

abstract base class for a tree with an Parameterized interface

provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)

This class logarithmically transforms tree parameters.

constructs a neighbor-joining tree from pairwise distances

Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.

constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees

Deprecated.

Neighbour-joining tree construction based on a distance matrix

UPGMA tree construction based on a distance matrix

Takes a tree (in generation units) and returns a scaled version of it (in mutation units).

The cheapy copy that just creates a SimpleTree

Obtains every rooting of a base tree

Root a tree around it's midpoint.

Generates a tree which is identical to baseTree but has attributes (defined by attributeName) at all internal nodes excluding the root node signifying (as a value between 0 and 100) the replicate support by clade (that is the proportion of replicates that produce the sub clade under that node)

Roots a tree by an outgroup

Takes a tree and returns a scaled version of it.

Takes a tree and returns a scaled version of it.

Unroot a tree (makes the base of the tree a trification).

Takes a tree (in mutation units) and returns a scaled version of it (in generation units).

Read a tree from an input source.

Deprecated.

Extracts an alignment from a tree.

Extracts a time order character data from a tree.

Generate an array of simulated alignments based on an array of input trees

Takes a tree (in generation units) and returns a scaled version of it (in mutation units).

Roots a tree by an outgroup

creates a clade system from a tree (using a pre-specified order of sequences)

Obtains every rooting of a base tree

Returns the mid point rooting of a tree.

Returns a uniformly distributed random node from the tree, including both internal and external nodes.

computes Robinson-Foulds (1981) distance between two trees

computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1

Root a tree by an outgroup.

Roots a tree by an outgroup

Takes a tree and returns a scaled version of it.

Takes a tree and returns a scaled version of it.

creates a split system from a tree (using tree-induced order of sequences)

Unroot a tree (makes the base of the tree a trification).

map external identifiers in the tree to a set of given identifiers (which can be larger than the set of external identifiers but must contain all of them) NOTE: for efficiency it is assumed that the node lists of the tree are correctly maintained.

Operates on input tree.

print a this tree in New Hampshire format (including distances and internal labels)

Rotates branches by leaf count.

Deprecated.

take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

clone constructor

clone constructor

compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)

compute induced distance matrix using actual branch lengths

Construct a TreeManipulator based around a normal tree

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

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

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

Calculate the log likelihood of a particular set of phylogenetic data

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