Tag: Evolution

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

MBEToolbox 3.0 – MATLAB Molecular Biology & Evolution Toolbox

MBEToolbox 3.0

:: DESCRIPTION

MBEToolbox is a tool which aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned Matlab users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MBEToolbox

:: MORE INFORMATION

Citation:

James J Cai, David K Smith, Xuhua Xia, Kwok-yung Yuen.
MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution
Evolutionary Bioinformatics Online 2006, 2 189-192

SBEToolbox 1.3.3 – MATLAB Systems Biology & Evolution Toolbox

SBEToolbox 1.3.3

:: DESCRIPTION

SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven GUI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne), compute various network topology measures etc…

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBEToolbox

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. eCollection 2013.
SBEToolbox: A Matlab Toolbox for Biological Network Analysis.
Konganti K1, Wang G, Yang E, Cai JJ.

FFPopSim 2.0 – Forward Simulation package for the Evolution of large Populations

FFPopSim 2.0

:: DESCRIPTION

FFPopSim (Fast Forward Population Genetic Simulation) is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution.

::DEVELOPER

FFPopSim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler
  • Python

:: DOWNLOAD

 FFPopSim

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3332-3. doi: 10.1093/bioinformatics/bts633. Epub 2012 Oct 24.
FFPopSim: an efficient forward simulation package for the evolution of large populations.
Zanini F, Neher RA.

SpideR 1.5.0 – SPecies IDentity and Evolution in R

SpideR 1.5.0

:: DESCRIPTION

Spider is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation.

::DEVELOPER

SpideR team

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 SpideR

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2012 May;12(3):562-5. doi: 10.1111/j.1755-0998.2011.03108.x. Epub 2012 Jan 16.
Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.
Brown SD1, Collins RA, Boyer S, Lefort MC, Malumbres-Olarte J, Vink CJ, Cruickshank RH.

CLIME v1.1 Beta – Clustering by Inferred Models of Evolution OMIM results

CLIME v1.1 Beta

:: DESCRIPTION

CLIME is an algorithm that partitions an input gene set of interest into distinct, evolutionarily conserved modules (ECMs). It then expands each module with genes sharing an inferred evolutionary history.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOS

:: DOWNLOAD

CLIME

:: MORE INFORMATION

Citation

Li Y, Calvo SE, Gutman R, Liu JS, Mootha VK.
Expansion of biological pathways based on evolutionary inference.
Cell. 2014 Jul 3;158(1):213-25. doi: 10.1016/j.cell.2014.05.034. PMID: 24995987; PMCID: PMC4171950.

TREND – Platform for Protein Evolution and Function Analysis

TREND

:: DESCRIPTION

TREND (TRee-based Exploration of Neighborhoods and Domains) is a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses

::DEVELOPER

ZhulinLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Gumerov VM, Zhulin IB.
TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses.
Nucleic Acids Res. 2020 Jul 2;48(W1):W72-W76. doi: 10.1093/nar/gkaa243. PMID: 32282909; PMCID: PMC7319448.

Methclone v2 – Dynamic Evolution of Clonal Epialleles

Methclone v2

:: DESCRIPTION

Methclone detects the dynamic evolution of clonal epialleles in DNA methylation sequencing data.

::DEVELOPER

The Jackson Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Methclone

:: MORE INFORMATION

Citation

Genome Biol. 2014 Sep 27;15(9):472. doi: 10.1186/s13059-014-0472-5.
Dynamic evolution of clonal epialleles revealed by methclone.
Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D’Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE.