PAL 1.5.1 – Java Library for Molecular Evolution & Phylogenetics

PAL 1.5.1

:: DESCRIPTION

PAL (Phylogenetic Analysis Library) 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.

::DEVELOPER

PAL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

PAL

:: MORE INFORMATION

Citation

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

Vanilla 1.2 – Programs to Access Features in PAL

Vanilla 1.2

:: DESCRIPTION

Vanilla is a collection of command line programs written in Java to access some selected features in PAL, a Java library for molecular evolution and phylogenetics (see http://www.cebl.auckland.ac.nz/pal-project/ for details on PAL). Note that Vanilla does not provide all functionality available in PAL.

::DEVELOPER

Strimmer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

Vanilla

:: MORE INFORMATION

Citation

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

PAL 1.31 – Pseudoknot Aligment for RNA Sequences

PAL 1.31

:: DESCRIPTION

PAL is an implementation of an efficient algorithm to compute an optimal structural alignment of an RNA sequence against a genomic substring.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

PAL

:: MORE INFORMATION

Citation

J Comput Biol. 2008 Jun;15(5):489-504. doi: 10.1089/cmb.2007.0214.
Structural alignment of pseudoknotted RNA.
Han B, Dost B, Bafna V, Zhang S.