PHYLDOG – Organism and Gene PHYlogenies Modeling Gene Duplications and Losses

PHYLDOG

:: 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.

DLCoal 1.0 – Modeling Gene Duplications, Losses, and Coalescence

DLCoal 1.0

:: DESCRIPTION

DLCoal is a software package containing the DLCoalRecon program as well as several other useful utilities for working with gene trees.

DLCoalRecon  is a reconciliation method for inferring gene duplications, losses, and coalescence (incomplete lineage sorting).

::DEVELOPER

Matt Rasmussen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Python
  • GSL

:: DOWNLOAD

  DLCoal

:: MORE INFORMATION

Citation

Unified modeling of gene duplication, loss, and coalescence using a locus tree
Matthew D. Rasmussen and Manolis Kellis.
Genome Res. 2012 Apr;22(4):755-65.

LcaMap – Simultaneous Identification of Duplications, Losses and Lateral Gene Transfers

LcaMap

:: DESCRIPTION

LcaMap is a software for simultaneous identification of duplication, losses and lateral gene transfers. LcaMap takes a gene tree G, a species tree S, and the costs of a lateral gene transfer, a gene duplication, and a gene loss as its input. It outputs all minimum-cost LCA-reconciliations between G and S.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 LcaMap

:: MORE INFORMATION