:: DESCRIPTION
MimicrEE (Mimicing Experimental Evolution) is a tool for forward simulations of entire genomes. It basically allowes to simulate adaptation from standing genetic variation, thus no ‘de novo’ mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs.
DEVELOPER
Institute of Population Genetics, University of Veterinary Medicine Vienna
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SLiM (Selection on Linked Mutations) is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
Citation
SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model.
Haller BC, Messer PW.
Mol Biol Evol. 2019 Mar 1;36(3):632-637. doi: 10.1093/molbev/msy228.
:: DESCRIPTION
PSIKO (Population Structure Inference using Kernel-pca and Optimisation) is a software tool written in C++ for quick and accurate estimation of individual ancestry coefficients of a dataset exhibiting population structure.
::DEVELOPER
The UEA Computational Biology Laboratory at the University of East Anglia (UEA)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS.
Popescu AA, Huber KT.
Bioinformatics. 2015 Jul 2. pii: btv396.
:: DESCRIPTION
SANTA-SIM is a forward-time simulator for gene sequences modeling a variety of mutation and selection processes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.
Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen Iv FA, Theys K.
Virus Evol. 2019 Mar 8;5(1):vez003. doi: 10.1093/ve/vez003.
:: DESCRIPTION
ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ngsTools: methods for population genetics analyses from next-generation sequencing data.
Fumagalli M, Vieira FG, Linderoth T, Nielsen R.
Bioinformatics. 2014 May 15;30(10):1486-7. doi: 10.1093/bioinformatics/btu041.
:: DESCRIPTION
GENEPOP is a population genetics software package
::DEVELOPER
Michel Raymond (Raymond@isem.univ-montp2.fr) and Francois Rousset (Rousset@isem.univ-montp2.fr)
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rousset, F., 2008.
Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux.
Mol. Ecol. Resources 8: 103-106.
:: DESCRIPTION
GONe (Generational Overlap Ne) is a user-friendly, Windows-based program for estimating effective size (Ne) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age-structure in populations.
::DEVELOPER
Jason Coombs ,jcoombs@cns.umass.edu ,Ben Letcher, and Keith Nislow
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GONe: software for estimating effective population size in species with generational overlap.
Coombs JA, Letcher BH, Nislow KH.
Mol Ecol Resour. 2012 Jan;12(1):160-3. doi: 10.1111/j.1755-0998.2011.03057.x
:: DESCRIPTION
DistMiss computes a matrix of genetic distances between populations on the basis of their allele frequencies at L loci.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MDIV is a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). The program can be used to test if there is evidence for migration between two populations or evidence for shared recent common ancestry. In addition, you get maximum likelihood estimates of the demographic parameters.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genetics. 2001 Jun;158(2):885-96.
Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
Nielsen R, Wakeley J.
:: DESCRIPTION
ProSeq (PROcessor of SEQuences) is a program for sequence editing and population genetics (mol/evol) analysis.ProSeq is quite a convenient tool for sequence handling (correcting ABI chromatograms, contig assembly, hand correction of the alignments etc.) and preliminary molecular evolution analysis. However, it is recommended to check the results of the analyses by the other software since the program is under development and not all the parts of the program are thoroughly tested and completely reliable
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Filatov, D.A. (2009)
Processing and population genetic analysis of multigenic datasets with ProSeq3 software
Bioinformatics. 25 (23): pp 3189-3190.
