Packages 
Package Description
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.