Tag: Genome Evolution

NU-IN 1.0.3 – Simulate Gene and Genome Evolution

NU-IN 1.0.3

:: DESCRIPTION

The NU-IN extension module is a extension to EvolSimulator. With the NU-IN module, users are now able to simulate both drift and selection at the nucleotide, amino acid, copy number, and gene family levels across sets of related genomes, for user-specified starting sequences and associated parameters.

::DEVELOPER

The Dlugosch Lab @ The University of Arizona

:: SCREENSHOTS

N/A

::  REQUIREMENTS

:: DOWNLOAD

 NU-IN

:: MORE INFORMATION

Citation

BMC Res Notes. 2010 Aug 2;3:217. doi: 10.1186/1756-0500-3-217.
NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform.
Dlugosch KM, Barker MS, Rieseberg LH.

ALF 1.0 – Simulation Framework for Genome Evolution

ALF 1.0

:: DESCRIPTION

ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement.

::DEVELOPER

ALF team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Mac /  Linux

:: DOWNLOAD

 ALF

:: MORE INFORMATION

Citation

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz:
ALF – A Simulation Framework for Genome Evolution.
Mol Biol Evol, 29(4):1115-1123, April 2012.

EvolSimulator 2.1.0 – Simulation Test Bed for Hypotheses of Genome Evolution

EvolSimulator 2.1.0

:: DESCRIPTION

EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 EvolSimulator

:: MORE INFORMATION

Citation

Beiko, R.G. and Charlebois, R.L. (2007).
A simulation test bed for hypotheses of genome evolution.
Bioinformatics 23:825-831.