Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Research » Publications at this Location » Publication #156857
Title: A BRIEF INTRODUCTION TO THE PHYLOGENETIC ANALYSIS LIBRARY, VERSION 1.5

Author
item GOODE, MATTHEW - UNIVERSITY OF AUCKLAND
item STRIMMER, KORBINIAN - UNIVERSITY OF MUNICH
item DRUMMOND, ALEXEI - OXFORD UNIVERSITY
item Buckler, Edward - Ed
item RODRIGO, ALLEN - UNIVERISITY OF AUCKLAND

Submitted to: Conferences in Research and Practice in Information Technology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2003
Publication Date: 1/14/2004
Citation: Goode, M., Strimmer, K., Drummond, A., Buckler Iv, E.S., Rodrigo, A. 2004. A brief introduction to the phylogenetic analysis library, version 1.5. Conferences in Research and Practice in Information Technology. 29:175-179.

Interpretive Summary: Molecular genomics is providing a wealth of data on the diversity of organisms. The Phylogenetic Analysis Library (PAL) is a data analysis package that includes the programming tools necessary to deal with these massive datasets. By participating in the development of these basic tools and utilizing them in our work, we are better able to evaluate the enormous diversity of plant germplasm. PAL can be accessed at http://www.cebl.auckland.ac.nz/pal-project.

Technical Abstract: The Phylogenetic Analysis Library (PAL) is an ongoing and open project to develop a powerful programming toolkit for phylogenetic analysis using the Java language. Available at http://www.cebl.auckland.ac.nz/pal-project, PAL is intended for use by developers of phylogenetic applications, as well as bioinformatics researchers who require a more programmatic approach than the user interface or scripting abilities that other packages can provide. Replacing version 1.1 is the newer version 1.5, which adds a number of features designed to enhance existing methods of molecular sequence analysis without sacrificing simplicity and ease of use. Future releases with new and improved applications are planned, and PAL users are encouraged to submit their own changes.