Literature DB >> 11448888

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

A Drummond1, K Strimmer.   

Abstract

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. AVAILIABILTY: 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.

Mesh:

Year:  2001        PMID: 11448888     DOI: 10.1093/bioinformatics/17.7.662

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  61 in total

1.  Inferring confidence sets of possibly misspecified gene trees.

Authors:  Korbinian Strimmer; Andrew Rambaut
Journal:  Proc Biol Sci       Date:  2002-01-22       Impact factor: 5.349

2.  Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.

Authors:  Jason Raymond; Olga Zhaxybayeva; J Peter Gogarten; Robert E Blankenship
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2003-01-29       Impact factor: 6.237

3.  An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.

Authors:  Ignacio Maeso; Manuel Irimia; Juan J Tena; Esther González-Pérez; David Tran; Vydianathan Ravi; Byrappa Venkatesh; Sonsoles Campuzano; José Luis Gómez-Skarmeta; Jordi Garcia-Fernàndez
Journal:  Genome Res       Date:  2012-01-10       Impact factor: 9.043

4.  GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis.

Authors:  Vikas R Pejaver; Jaehyun An; Sungmin Rhee; Ankita Bhan; Jeong-Hyeon Choi; Boshu Liu; Heewook Lee; Pamela J Brown; David Kysela; Yves V Brun; Sun Kim
Journal:  Bioinformatics       Date:  2012-04-11       Impact factor: 6.937

5.  Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean.

Authors:  Kimberly P Tucker; Rachel Parsons; Erin M Symonds; Mya Breitbart
Journal:  ISME J       Date:  2010-12-02       Impact factor: 10.302

6.  Molecular characterization of two endothelin pathways in East African cichlid fishes.

Authors:  Eveline T Diepeveen; Walter Salzburger
Journal:  J Mol Evol       Date:  2012-01-21       Impact factor: 2.395

7.  Ancient gene duplications and the root(s) of the tree of life.

Authors:  Olga Zhaxybayeva; Pascal Lapierre; J Peter Gogarten
Journal:  Protoplasma       Date:  2005-12-30       Impact factor: 3.356

8.  Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.

Authors:  Olga Zhaxybayeva; J Peter Gogarten; Robert L Charlebois; W Ford Doolittle; R Thane Papke
Journal:  Genome Res       Date:  2006-08-09       Impact factor: 9.043

9.  TCP transcription factors predate the emergence of land plants.

Authors:  Olivier Navaud; Patrick Dabos; Elodie Carnus; Dominique Tremousaygue; Christine Hervé
Journal:  J Mol Evol       Date:  2007-06-12       Impact factor: 2.395

10.  Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level.

Authors:  Golo Ahlenstiel; Kirsten Roomp; Martin Däumer; Jacob Nattermann; Martin Vogel; Jürgen K Rockstroh; Niko Beerenwinkel; Rolf Kaiser; Hans-Dieter Nischalke; Tilman Sauerbruch; Thomas Lengauer; Ulrich Spengler
Journal:  Clin Vaccine Immunol       Date:  2007-08-22
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