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

:: 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

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