To our knowledge, PAL is the only project that aims at providing a collaborative Java library for molecular evolution and phylogenetics.

Similar "private" projects are, however, currently undertaken, e.g., by Andrew Rambaut and Mike Charleston (their Nautilus project) or by the Felsenstein lab (both in C++).

Other Java projects in molecular evolution and bioinformatics include:

• Mesquite, a modular system for evolutionary analysis is developed by Wayne Maddison and David Maddison. Mesquite is designed to allow third-party components and plug-in modules and provides a nice graphical user interface.
• The BioJava project is collaborative project that aims at creating a Java library for general bioinformatics applications (BLAST, CORBA etc.).
• Christian Zmasek's program FORESTER (BSD license) is a Java project aimed at phylogenomics. ATV is part of FORESTER and is a useful tree viewer that can also displays trees written in the NHX format (an extended NH format).
• John Brzustowski distributes qclust, a set of Java classes implementing a variety of clustering methods, including UPGMA and neighbor-joining.
• Ed Buckler has developed a number of Java applications for phylogenetic and linkage analysis (e.g., Phylogeographer and TASSEL ). Ed is now a co-developer of PAL.
• Don Gilbert distributes a number of his Java programs in his IUBio Archive, for example the sequence editor SeqPup and the tree drawing program Phylodendron.
• David Posada and collaborators have written GEODIS, a Java program for cladistic nested analysis of the geographical distribution of genetic haplotypes, and TCS, a Java program to estimate gene genealogies using statistical parsimony.

Finally, the general issue of scientific programming in Java is discussed, e.g., on the Java Numerics web page.