PAL: Phylogenetic Analysis Library

A Java library for molecular evolution and phylogenetics
Version 1.4 (January 20, 2002)

The PAL project (http://www.pal-project.org) is a collaborative effort dedicated to provide a high quality Java library for use in molecular evolution and phylogenetics.

This package may be distributed under the terms of the GNU Lesser General Public License

Copyright (c) 1999-2002 PAL Development Core Team.

Core Team (with CVS rights):

Alexei Drummond (2000-)
email: [email protected]
School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand.

Ed Buckler (2001-)
email: [email protected]
Department of Genetics, North Carolina State University, 2523 Gardner Hall, Box 7614, Raleigh, NC 27695-7614, USA.

Korbinian Strimmer (1999-)
email: [email protected]
Department of Statistics, University of Munich, Ludwigstrasse 33, 80539 Munich, Germany.

Other Contributions:

Matthew G. Goode, University of Auckland (GUI, codon and alignment classes, utilities)
Sean Luke, University of Maryland (Random number generator)
Oliver G. Pybus, University of Oxford (Demographic models)
Andrew Rambaut, University of Oxford (Yang codon model, demographic models)
Jesse Stone, ? (Optimization code)

Overview:

The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces in 16 packages with a total of more than 35,000 lines of Java code. Please refer to the API documentation for a detailed description of all classes and methods available, and to the release history for an overview of the development history of PAL.

Please feel free to use PAL or parts of it in your own programs, the terms and conditions for copying, distribution and modification of the GNU Lesser General Public License apply. (Note that previous versions of PAL were licensed under the GNU GPL rather the GNU LGPL.)

Contributing code to PAL is greatly encouraged, please read the following guidelines.

If you wish to cite PAL please use

Drummond, A., and K. Strimmer. 2001. PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17: 662-663.

This paper provides an overview over PAL version 1.1.
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User Interfaces:

PAL is designed as an object-oriented programming library, and as such it has no direct user interface. To access the methods and objects available in PAL you need to program in Java.

However, there are user-friendly programs available that rely (in part) on PAL to do their job. Be aware, however, that they will usually restrict functionality to some core features of PAL:

• Vanilla aims at providing a simple bare bones text interface to some selected features in PAL. It basically consists of a set of command line applications, most of them in PHYLIP CUI style. Best run in a UNIX (incl. MacOS X) or MSDOS shell. This package is also useful to see how you could use PAL in your own program.
• Pebble (codenamed vCEBL) is much more broadly targeted. It not only offers a GUI interface to PAL but also comes with its own functional command language. PEBBLE has an easy-to-use installation program.

• It should be rather straightforward to use features available in PAL from within the Mesquite program, a modular system for evolutionary analysis written in Java by Wayne and Dave Maddison.
• In collaboration with Andrew Rambaut (University of Oxford) it is planned to develop a general XML interface definition for evolutionary analysis, which will be implemented for PAL and for Andrew Rambaut 's Nautilus C++ libraries.
• Java provides the opportunity to write web-based applications (applets) that can be executed in a web browser. In collaboration with Andrew Rambaut it is planned to write simple applets, e.g. for skyline plot analysis, tree viewing etc.

Main Features:

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)
• ...

Download and Installation:

By design, PAL can be installed and run on any platform where Java 1.1 (or better) is available.

PAL is distributed in two variants, one for Unix/MSDOS (includes makefiles for jikes/gcj) and one for Macintosh (includes project file for CW 6):

• pal-1.4.tar.gz
• pal-1.3.hqx (unfortunately, for the moment we cannot provide a Mac version of PAL 1.4)

• http://iubio.bio.indiana.edu/soft/molbio/java/pal

After uncompressing using appropriate tools the following simple directory structure will be created:

	             pal-1.4
                  ______|______
                 |             |                
                doc           src                

To actually compile the sources you need to set the class path properly to the folder "pal-1.4/src". Please consult the manual for your Java development kit (or your system administrator) for details.

Compile of PAL into native code on Unix has been successfully tested using the following software (or any later version):

• gcc 2.95.2 (contains gcj)
• libgcj 2.95.1(required by gcj)
• jikes 1.06 (Java bytecode compiler)

For compilation on Macintosh a Metrowerks Codewarrior project file (suitable for CW 6) is included.

Older versions of PAL are also available, please refer to the release history.
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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:

• 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.
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Acknowledgments:

We thank Oliver Pybus, Andrew Rambaut, Rick Ree, Allen Rodrigo, and Wayne Maddison for discussion and valuable suggestions. We also thank Allen Rodrigo for providing hardware through his NIH grant #59174 and Don Gilbert for distributing PAL in his software archive. This work is also supported by a Bright Future´s Scholarship of FRST to A.D. and an Emmy-Noether-Fellowship of the DFG to K.S.
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