CellLine – Stochastic Cell Lineage Simulator

CellLine

:: DESCRIPTION

CellLine is a simulator of the dynamics of gene regulatory networks (GRN) in the cells of a lineage. From user-defined reactions and initial substance quantities, it generates cell lineages, i.e. genealogic pedigrees of cells related through mitotic division. Each cell’s dynamics is driven by a delayed stochastic simulation algorithm (delayed SSA), allowing multiple time delayed reactions.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

CellLine

:: MORE INFORMATION

Citation:

Andre S. Ribeiro, Daniel A. Charlebois, Jason Lloyd-Price,
“CellLine, a stochastic cell lineage simulator“,
Bioinformatics, (accepted), Sept. 2007.

Nemo 2.3.51 – A Stochastic, Individual-base, Genetically Explicit Simulation Platform

Nemo 2.3.51

:: DESCRIPTION

Nemo is a forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of life history/phenotypic traits and population genetics in a flexible (meta-)population framework.

::DEVELOPER

Frédéric Guillaume

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/ MacOsX

:: DOWNLOAD

Nemo

:: MORE INFORMATION

Citation

Guillaume, F., and J. Rougemont. 2006.
Nemo: an evolutionary and population genetics programming framework.
Bioinformatics 22:2556-2557.

SIMMAP 1.5.2 – StochastIc Mutational MApping on Phylogenies

SIMMAP 1.5.2

:: DESCRIPTION

SIMMAP is a post tree analysis GUI software package for stochastically mapping mutations on phylogenies.SIMMAPimplements stochastic mutational mapping using a wide range of models: 4 x 4 general reversible nucleotide models and standard Mk character models. SIMMAP allows addressing a variety of evolutionary questions. Specifically, questions about the number, type and placement of mutations on a phylogeny. In addition, tests of character correlation, positive selection, and ancestral states are available.

::DEVELOPER

Jonathan P Bollback

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX

:: DOWNLOAD

SIMMAP

:: MORE INFORMATION

Citation

SIMMAP: stochastic character mapping of discrete traits on phylogenies.
Bollback JP.
BMC Bioinformatics. 2006 Feb 23;7:88.