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.

CisEvolver – Molecular Evolution Simulation Program

CisEvolver 0.4

:: DESCRIPTION

CisEvolver is a molecular evolution simulation program

::DEVELOPER

Eisen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CisEvolver

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.
Large-scale turnover of functional transcription factor binding sites in Drosophila.
Moses AM1, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.

TipDate 1.2 – Estimate the rate of Molecular Evolution

TipDate 1.2

:: DESCRIPTION

TipDate is a program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences.

::DEVELOPER

Andrew Rambaut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borwser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Andrew Rambaut, 2000.
Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies.
Bioinformatics. 16: 395-399.

Phylemon 2.0 – Web-tools for Molecular Evolution, Phylogenetics, Phylogenomics and Hypothesis testing

Phylemon 2.0

:: DESCRIPTION

Phylemon is the suite of web-tools for molecular evolution, phylogenetics and phylogenomics. It is conceived as a natural response to the increasing demand of data analysis of experimental scientists seeking to add molecular evolution and phylogenetic insight into their research.

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No, Only Web Service

:: MORE INFORMATION

Citation

Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W470-4. Epub 2011 Jun 6.