Packages

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