All Classes

abstract base class for all rate matrices

As of 2006-12-06, this interface is not used anywhere in JEBL, and it doesn't have any implementing classes.

base class of rate matrices for amino acids

Interface for associating attributeNames with an object.

Common implementation of Attributable interface used by Nodes.

A default implementation of the Sequence interface.

Binomial coefficients

Date: 15/01/2006 Time: 10:13:50

Created by IntelliJ IDEA.

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

Stores a set of unique clades for a tree

A likelihood function for the coalescent.

As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see Codons.

A ProgressListener that is suitable for a task that consists of several subtasks.

A TreeBuilder that builds a consensus tree for a set of trees on identical leaf sets.

This class models coalescent intervals for a constant population (parameter: N0=present-day population size).

This class models logistic growth from an initial population size.

This interface provides methods that describe a demographic function.

Represents a node in a graph or tree.

This class models exponential growth from an initial ancestral population size.

This class models logistic growth from an initial exponential phase.

Class for exporting a fasta file format.

Class for reconstructing characters using Fitch parsimony.

gamma function

A set of standard genetic codes.

This class is thrown by getEdgeLength(node1, node2) if node1 and node2 are not directly connected by an edge.

Compute HKY corrected distance matrix

A sequence importer sending the sequences back one by one, which makes it possible to import larger documents if handled wisely on the other side.

A concrete class for a set of coalescent intevals.

Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.

This class models logistic growth.

compute matrix exponential and, subsequently, transition probabilities for a given rate matrix

A tri-state boolean value that can also be "Maybe" besides True and False.

interface for a classes that wish to monitor the progress of a Minimiser

Given a set of trees determine the most probable trees, i.e.

interface for a function of several variables

A factory interface for MultivariateMinimums (because they aren't statefree)

Constructs an unrooted tree by neighbor-joining using pairwise distances.

Class for importing NEXUS file format.

Represents the block types used in the nexus format

Performs recursive local alignments.

An interface for a numerical column in a log.

Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.

converts a multivariate function into a univariate function by keeping all but one argument constant

An interface representing a set of site patterns.

Class for importing PHYLIP sequential file format

Random number generation.

A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.

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.