Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (53)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Drummond, A.
Right arrow Articles by Strimmer, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Drummond, A.
Right arrow Articles by Strimmer, K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 17 no. 7 2001
Pages 662-663
© 2001 Oxford University Press

Applications Note

PAL: an object-oriented programming library for molecular evolution and phylogenetics

Alexei Drummond 1 and Korbinian Strimmer 2,*

1 School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
2 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK

Received on January 20, 2001 ; accepted on March 15, 2001

Summary: Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers.

Availability: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.

Contact: a.drummond{at}auckland.ac.nz; korbinian.strimmer{at}zoo.ox.ac.uk

Supplementary information: An online description of the Application Programming Interface (API) of all public classes in PAL is available at http://www.pal-project.org/api/.

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
S. D'Aniello, M. Irimia, I. Maeso, J. Pascual-Anaya, S. Jimenez-Delgado, S. Bertrand, and J. Garcia-Fernandez
Gene Expansion and Retention Leads to a Diverse Tyrosine Kinase Superfamily in Amphioxus
Mol. Biol. Evol., September 1, 2008; 25(9): 1841 - 1854.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
J. J. Cai
PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution
J. Hered., February 29, 2008; (2008) esm127v1.
[Abstract] [Full Text] [PDF]

Home page
 CVIHome page
G. Ahlenstiel, K. Roomp, M. Daumer, J. Nattermann, M. Vogel, J. K. Rockstroh, N. Beerenwinkel, R. Kaiser, H.-D. Nischalke, T. Sauerbruch, et al.
Selective Pressures of HLA Genotypes and Antiviral Therapy on Human Immunodeficiency Virus Type 1 Sequence Mutation at a Population Level
Clin. Vaccine Immunol., October 1, 2007; 14(10): 1266 - 1273.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. M. Keane, T. J. Naughton, and J. O. McInerney
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W33 - W37.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
F. Abascal, D. Posada, and R. Zardoya
MtArt: A New Model of Amino Acid Replacement for Arthropoda
Mol. Biol. Evol., January 1, 2007; 24(1): 1 - 5.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Buendia and G. Narasimhan
Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
Bioinformatics, September 15, 2006; 22(18): 2313 - 2314.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
C.-C. Hon, T.-Y. Lam, A. Drummond, A. Rambaut, Y.-F. Lee, C.-W. Yip, F. Zeng, P.-Y. Lam, P. T. W. Ng, and F. C. C. Leung
Phylogenetic Analysis Reveals a Correlation between the Expansion of Very Virulent Infectious Bursal Disease Virus and Reassortment of Its Genome Segment B.
J. Virol., September 1, 2006; 80(17): 8503 - 8509.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
J. E. Stajich and H. Lapp
Open source tools and toolkits for bioinformatics: significance, and where are we?
Brief Bioinform, September 1, 2006; 7(3): 287 - 296.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
O. Zhaxybayeva, J. P. Gogarten, R. L. Charlebois, W. F. Doolittle, and R. T. Papke
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
Genome Res., September 1, 2006; 16(9): 1099 - 1108.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. L. Robertson and A. Tartar
Evolution of Glutamine Synthetase in Heterokonts: Evidence for Endosymbiotic Gene Transfer and the Early Evolution of Photosynthesis
Mol. Biol. Evol., May 1, 2006; 23(5): 1048 - 1055.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Abascal, R. Zardoya, and D. Posada
ProtTest: selection of best-fit models of protein evolution
Bioinformatics, May 1, 2005; 21(9): 2104 - 2105.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. M. Keane, T. J. Naughton, S. A. A. Travers, J. O. McInerney, and G. P. McCormack
DPRml: distributed phylogeny reconstruction by maximum likelihood
Bioinformatics, April 1, 2005; 21(7): 969 - 974.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. L. K. Pond, S. D. W. Frost, and S. V. Muse
HyPhy: hypothesis testing using phylogenies
Bioinformatics, March 1, 2005; 21(5): 676 - 679.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. Cobbe and M. M. S. Heck
The Evolution of SMC Proteins: Phylogenetic Analysis and Structural Implications
Mol. Biol. Evol., February 1, 2004; 21(2): 332 - 347.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
R. Forsberg and F. B. Christiansen
A Codon-Based Model of Host-Specific Selection in Parasites, with an Application to the Influenza A Virus
Mol. Biol. Evol., August 1, 2003; 20(8): 1252 - 1259.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
H. A. Ross, G. M. Lento, M. L. Dalebout, M. Goode, G. Ewing, P. McLaren, A. G. Rodrigo, S. Lavery, and C. S. Baker
DNA Surveillance: Web-Based Molecular Identification of Whales, Dolphins, and Porpoises
J. Hered., March 1, 2003; 94(2): 111 - 114.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, and W. Solomon
Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data
Genetics, July 1, 2002; 161(3): 1307 - 1320.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
U. Arnason, J. A. Adegoke, K. Bodin, E. W. Born, Y. B. Esa, A. Gullberg, M. Nilsson, R. V. Short, X. Xu, and A. Janke
Mammalian mitogenomic relationships and the root of the eutherian tree
PNAS, June 11, 2002; 99(12): 8151 - 8156.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
K. Strimmer and O. G. Pybus
Exploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot
Mol. Biol. Evol., December 1, 2001; 18(12): 2298 - 2305.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.