Packages
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. rate matrices (e.g., the HKY matrix) and rate heterogeneity distributions (e.g., the discrete Gamma distribution), as well as a class for conveniently computing transition probabilities.
pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
pal.util Utility classes for sorting etc.
pal.xml Utility classes for converting PAL objects to and from XML documents.