PAL: Phylogenetic Analysis Library
Related (Java) Projects
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:
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
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
and the tree drawing program
- David Posada and collaborators have written
a Java program for cladistic nested analysis of the geographical distribution
of genetic haplotypes,
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