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

seevolution

:: 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.

EvoFBA – Simulating Evolution of Constraint Based Models of Cellular Metabolism

EvoFBA

:: DESCRIPTION

EvoFBA is a MATLAB implementation of the evolutionary and ecological dynamics simulations of growing E.coli populations

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • MatLab

:: DOWNLOAD

EvoFBA

:: MORE INFORMATION

Citation

BMC Evol Biol, 16 (1), 163
Metabolic Modelling in a Dynamic Evolutionary Framework Predicts Adaptive Diversification of Bacteria in a Long-Term Evolution Experiment
Tobias Großkopf, Jessika Consuegra , Joël Gaffé, John C Willison, Richard E Lenski, Orkun S Soyer, Dominique Schneider

TFBS Evo 1.0 – Tracing the Evolution of Lineage-specific Transcription Factor Binding Sites

TFBS Evo 1.0

:: DESCRIPTION

TFBS Evo is a model which traces the evolution of lineage-specific transcription factor binding sites without relying on detailed base-by-base cross-species alignments.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TFBS Evo

:: MORE INFORMATION

Citation

Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.
Yokoyama KD, Zhang Y, Ma J.
PLoS Comput Biol. 2014 Aug 21;10(8):e1003771. doi: 10.1371/journal.pcbi.1003771.

dnet 1.1.5 – Integrative Analysis of Omics data in terms of Network, Evolution and Ontology

dnet 1.1.5

:: DESCRIPTION

dnet is an open-source R package for omics data integrative analysis in terms of network, evolution and ontology

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dnet

:: MORE INFORMATION

Citation:

Genome Med. 2014 Aug 26;6(8):64. doi: 10.1186/s13073-014-0064-8.
The ‘dnet’ approach promotes emerging research on cancer patient survival.
Fang H, Gough J

SPECTRE 1.1.5 – Suite of Phylogenetic tools for Reticulate Evolution

SPECTRE 1.1.5

:: DESCRIPTION

SPECTRE provides several new implementations of pre-published algorithms to construct phylogenetic trees and networks (more precisely split networks), along with an interactive graphical interface for visualizing planar split networks.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPECTRE 

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Mar 15;34(6):1056-1057. doi: 10.1093/bioinformatics/btx740.
SPECTRE: a suite of phylogenetic tools for reticulate evolution.
Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V.

PGEToolbox 3.0 – Matlab Toolbox for Population Genetics and Evolution

PGEToolbox 3.0

:: DESCRIPTION

PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  PGEToolbox

:: MORE INFORMATION

Citation:

Cai JJ (2008)
PGEToolbox: A Matlab toolbox for population genetics and evolution
Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127

SDSE 2.0 – Simulation of DNA Sequence Evolution

SDSE 2.0

:: DESCRIPTION

SDSE is an  algorithm  to  simulate  DNA  sequence  evolution  under  a  general  stochastic  model,  including  as  particular  cases  all  the  previously  used  schemes  of  nucleotide  substitution

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

SDSE

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 SDSE

:: MORE INFORMATION

Citation:

Comput Appl Biosci. 1989 Feb;5(1):47-50.
SDSE: a software package to simulate the evolution of a pair of DNA sequences.
Oliver JL, Marín A, Medina JR.

nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution

nhPhyML

:: DESCRIPTION

nhPhyML is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

  nhPhyML

:: MORE INFORMATION

Citation

Efficient likelihood computations with nonreversible models of evolution.
Boussau B, Gouy M.
Syst Biol. 2006 Oct;55(5):756-68.

MySSP 1.0.3.5 – Simulation of DNA Sequence Evolution across a Phylogenetic Tree

MySSP 1.0.3.5

:: DESCRIPTION

MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

MySSP

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MySSP

:: MORE INFORMATION

Citation

Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83