PAL is entirely written in the Java language. This allows for a clean object oriented design while avoiding the complexities of C++. Moreover, Java class code runs without needing recompilation on a wide range on platforms. Additionally, PAL also compiles into native code on Unix systems (just like C++) using the GNU compiler for Java (gcj), part of recent releases of the GNU compiler collection (gcc). Corresponding makefiles are included with this distribution of PAL.

PAL consists of a rich variety of objects to facilitate the construction of special-purpose tools for phylogenetic analysis. PAL contains, e.g., ready-to-use objects for:

• reading and writing sequence alignments, distance matrices, and trees
• a large variety of substitution models for nucleotides and amino acids (REV, TN, HKY, F84, F81, JC; Dayhoff, JTT, MTREV24, BLOSUM, VT, WAG, CPREV) as well as for codons (Yang codon model)
• Various models for rate variation over sites (invariable sites, Gamma)
• efficient maximum-likelihood estimation of pairwise distances and of branch lengths in a tree (for unconstrained, clock, and dated-tips clock trees)
• simulating coalescence intervals and estimation of demographic parameters
• likelihood ratio and chi-square tests and for comparison of phylogenetic hypotheses (e.g., Kishino-Hasegawa and Shimodaira-Hasegawa tests)
• manipulating alignments (e.g., bootstrapping) and trees and simulating data
• optimizing uni- and multivariate functions by various methods, computing numerical derivatives, random numbers (simulation quality), sorting etc.
• creating formatted input and output from/to files, standard io streams, and strings, through convenience classes that extend the standard Java IO library
• construct neighbor-joining, UPGMA and SUPGMA trees, and estimating least-squares branch lengths on trees (weighted and unweighted LS)
• translate nucleotide to AA sequences
• access mathematical special functions (gamma, error, binomial) and pdf, cdf, and quantile functions of statistical distributions (gamma, exponential, chi-square, normal, Pareto)
• create split systems from trees and compute partition distances between trees (Robinson-Foulds distance)
• XML interface for PAL objects (this uses the org.w3c.dom library which is included with PAL - please see the copyright info of this library)
• ...