iGTP 1.1 – Infer Species Phylogenies from Gene Phylogenies

iGTP 1.1

:: DESCRIPTION

iGTP is a program designed to help biologists infer species phylogenies from gene phylogenies, using the gene tree parsimony (GTP) approach. The program implements efficient heuristics which allows it to handle large-scale species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 iGTP

:: MORE INFORMATION

Citation

Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein,
iGTP: A software package for large-scale gene tree parsimony analysis“,
BMC Bioinformatics 2010, 11:574.

PHYLDOG 2.0beta – Organism and Gene PHYlogenies Modeling Gene Duplications and Losses

PHYLDOG 2.0beta

:: DESCRIPTION

Phyldog is a program made to simultaneously build gene and species trees when gene families have undergone duplications and losses.

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Boost libraries
  • Bio++

:: DOWNLOAD

 PHYLDOG

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):323-30. doi: 10.1101/gr.141978.112.
Genome-scale coestimation of species and gene trees.
Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V.