All Classes

abstract base class for all rate matrices

A command line interface for the algorithms in jebl.evolution.align.

Uninstantiable utility class with only static methods.

Stores a set of unique clades for a tree

Common implementation of Attributable interface used by Nodes.

A basic implementation of the Alignment interface.

A basic ProgressListener implementation that allows the caller to set the canceled status.

Billera tree distance - sum of change in branch lengths required to transform one tree to the second Note that this interface is not optimal for a large set where all pairs are required.

Similar to a StringBuilder, but its internal buffer is a byte[] with one entry for each character, so it can only correctly append single-byte characters.

Checks whether some operation has been cancelled; This will typically be used as a callback because it can only query whether a task has been cancelled, rather than cancel it (there is no cancel() method).

A default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to T

For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA.

An abstract base class for clustering algorithms from pairwise distances

This is a class that draws coalescent intervals under the given demographic function.

A codon implementation of the Sequence interface.

A memory efficient rooted tree.

Supported consensus methods.

This class models exponential growth from an initial population size.

This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).

Class for importing Fasta sequential file format.

A bit-set of fixed size.

A pair suitable for use in a HashMap.

What to do when an imported document contains illegal characters

A helper class for phylogenetic file format importers

An interface for a set of coalescent intevals.

Date: 17/01/2006 Time: 08:18:32

Compute jukes-cantor corrected distance matrix for a set of aligned sequences.

determines machine accuracy

* Export to MEGA.

abstract base class for minimisation of a multivariate function

A simple rooted tree providing some ability to manipulate the tree.

Export sequences and trees to Nexus format.

Thrown when a block is missing that is required for importing a particular type of data from the nexus input.

Represents a node in a graph or tree.

Uninstantiable utility class with only static methods.

approximates numerically the first and second derivatives of a function of a single variable and approximates gradient and diagonal of Hessian for multivariate functions

A means for describing odering information, and Utilities for creating such Orderings

minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.

An interface representing a list of states for a list of taxa (e.g.

Export alignment to Phylip format.

A decorator progress listener which delegates all method calls to an internal progress listener.

abstract base class for all rate matrices

A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..

Builds a distance matrix by performing a series of pairwise alignments between the specified sequences (unlike the methods in jebl.evolution.distances, which extract the pairwise distances from a multiple sequence alignment).

Interface for importers that do sequences

Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences.

A simple, and initially immutable rooted tree implementation.

utilities for split systems

This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.

Work in progress

Supported consensus methods.

Supported methods for tree building

A listener for notifying about changes to a tree or to the selected nodes in a tree.

Interface for importers that do trees

This class provides the framework for (backwards-through-time) tree simulation.

minimization of a real-valued function of one variable without using derivatives.

Provides some miscellaneous methods.