EVE – Evolution in Variable Environments

EVE

:: DESCRIPTION

The EVE software is a simulation framework for microbial populations in complex dynamic environments. The simulator allows the study of microbial evolution in multiple scales, ranging from network to meta-population level.

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
C++ Compiler

:: DOWNLOAD

EVE

:: MORE INFORMATION

Citation:

Science. 2008 Jun 6;320(5881):1313-7. doi: 10.1126/science.1154456.
Predictive behavior within microbial genetic networks.
Tagkopoulos I, Liu YC, Tavazoie S.

PSPE – Simulate Evolution of Non-coding DNA Sequences

PSPE

:: DESCRIPTION

PSPE (Phylogenetic Simulation of Promoter Evolution) is a computational tool specifically designed for simulating evolution of non-coding DNA sequences, in particular promoter sequences.

::DEVELOPER

PSPE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PSPE

:: MORE INFORMATION

Citation

Weichun Huang, Joseph R Nevins, and Uwe Ohler,
Phylogenetic simulation of promoter evolution: estimation and modelling of binding site turnover events and assessing their impact on alignment tools,
Genome Biology, Vol 8 (10) 2007

motifStack 1.34.0 – Visualization of Motif Alignment and the analysis of Transcription Factor Binding site Evolution

motifStack 1.34.0

:: DESCRIPTION

motifStack is a package for the visualization of the alignment of motifs as a phylogenetic tree in different layout types. This tool facilitates the analysis of binding site diversity and conservation within families of TFs and the evolution of TFs among different species. motifStack can align DNA motifs; generate motif signatures for closely related motifs; and plot aligned motifs as a stack, a linear or a radial tree, or a word cloud of sequence logos. Different parameter settings can be used to generate diverse types of plots with color schema highlighting important data features.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
BioConductor
R package

:: DOWNLOAD

motifStack

:: MORE INFORMATION

Citation:

Ou J, Wolfe SA, Brodsky MH, Zhu LJ.
visualization of motif alignment and the analysis of transcription factor binding site evolution for the analysis of transcription factor binding site evolution.
Nat Methods. 2018 Jan 3;15(1):8-9. doi: 10.1038/nmeth.4555. PMID: 29298290.

Drifter – Simulates Allele Frequencies using Forward-in-time Evolution under the Wright-Fisher model

Drifter

:: DESCRIPTION

Drifter simulates a forward-in-time Wright-Fisher model, and can be used to model genetic drift and explore the effects of sampling error given user-defined genetic frequency data.

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX /Windows
Perl

:: DOWNLOAD

Drifter

:: MORE INFORMATION

Citation

Cox, M.P. 2006.
Extreme Patterns of Variance in Small Populations: Placing Limits on Human Y-Chromosome Diversity through Time in the Vanuatu Archipelago.
Annals of Human Genetics 71:390-406.

Microsat – Simulates the Evolution of Linked and unlinked Microsatellites using the Coalescent

Microsat

:: DESCRIPTION

Microsat reads coalescent genealogies generated by Richard Hudson’s ms, and translates them into short tandem repeat (STR, or microsatellite) datasets using the single step mutation model (SMM).

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler

:: DOWNLOAD

Microsat

:: MORE INFORMATION

Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04

:: DESCRIPTION

Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

Crann

:: MORE INFORMATION

Citation:

Creevey, C. and J. O. McInerney (2003).
CRANN: Detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics (2003) 19: 1726.

DeCo – Evolution of Gene Neighborhoods

DeCo

:: DESCRIPTION

The software DeCo computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications and losses. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) gene trees which leaves are the extant genes. It outputs ancestral species, genes, and adjacencies. It also highlights the duplications involving several genes.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Bio++

:: DOWNLOAD

DeCo

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):i382-i388. doi: 10.1093/bioinformatics/bts374.
Evolution of gene neighborhoods within reconciled phylogenies.
Bérard S, Gallien C, Boussau B, Sz?ll?si GJ, Daubin V, Tannier E.

GEvolutionS – Genome Evolution Simulation

GEvolutionS

:: DESCRIPTION

GEvolutionS simulates an evolutionary Genome rearrangement scenario with different genome rearrange operations. It operates on the most general model of genomes with a mixed collection on linear and circular genomes. The simulation process includes all classical rearrangement operations such as dcj, fissions, fusions, inversions, translocations, transpositions with choosable quantum.

::DEVELOPER

N/A

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Mac / Windows
Java

:: DOWNLOAD

GEvolutionS

:: MORE INFORMATION

N/A

BEGFE 1.1 – Bayesian Estimation of Gene Family Evolution

BEGFE 1.1

:: DESCRIPTION

BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and death rate parameters and the numbers of gene copies at the internodes of the phylogenetic tree. In addition, BEGFE can simulate gene family data under the birth and death model.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX/ Windows

:: DOWNLOAD

BEGFE

:: MORE INFORMATION

Citation

Liu, L., L. Yu, V. Kalavacharla, Z. Liu.
A Bayesian model for gene family evolution.
BMC Bioinformatics. 2011, 12:426

Seevolution 1.1.2 – Time Machine for Evolution

Seevolution 1.1.2

:: DESCRIPTION

Seevolution is an interactive viewer for mutations occurring during genome evolution.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux /MacOsX/ Windows
Java
Java 3D

:: DOWNLOAD

Seevolution

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Apr 1;25(7):960-1. doi: 10.1093/bioinformatics/btp096.
Seevolution: visualizing chromosome evolution.
Esteban-Marcos A, Darling AE, Ragan MA.