Packages
Package
Description
 
Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.
Classes to model population genetic processes using the coalescent.
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).
Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
GUI components for some special objects (e.g., trees).
Classes for simple (formatted) input/output from/to files, strings and standard-in/out streams.
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials, random numbers, special function etc.
Classes for the analysis of "measurably evolving populations" (mep).
Classes that don't fit elsewhere ;^)
Classes for providing 'classical' population genetics analyses.
Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
Classes describing substitution models, i.e.
 
Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
 
Utility classes for sorting etc.
Utility classes for converting PAL objects to and from XML documents.