:: DESCRIPTION
Sunflower is an evolutionary model for promoters, analogous to the commonly used synonymous/nonsynonymous mutation models for protein-coding sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hoffman MM, Birney E. 2010.
An effective model for natural selection in promoters.
Genome Res. 20(5):685-692.
:: DESCRIPTION
HKA is a computer program that carries out the widely used statistical test for natural selection.This program can handle very large numbers of loci and sample sizes, and conducts tests via coalescent simulation as well as by the conventional chi square approximation. The simulations can also be used to conduct other tests of natural selection, including tests of Tajima’s D statistic (1989) and the D statistic of Fu and Li (1993).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TreeSelect is a software package for inferring natural selection from unusual population differentiation between closely related populations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bhatia et al. (2011),
“Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection“,
American Journal of Human Genetics, 89(3):368-381.
:: DESCRIPTION
SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genetics. 2013 Sep;195(1):181-93. doi: 10.1534/genetics.113.152587. Epub 2013 Jun 14.
Learning natural selection from the site frequency spectrum.
Ronen R, Udpa N, Halperin E, Bafna V.
:: DESCRIPTION
INSIGHT is a method for inferring signatures of recent natural selection from patterns of polymorphism and divergence across a collection of short dispersed genomic elements.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gronau I, Arbiza L, Mohammed J, Siepel A.
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence.
Mol Biol Evol. 2013 May;30(5):1159-71. doi: 10.1093/molbev/mst019. Epub 2013 Feb 5. PMID: 23386628; PMCID: PMC3697874.
:: DESCRIPTION
BayeScan ( (BAYEsian genome SCAN for outliers) ) aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. One of the scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient. Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations
::DEVELOPER
Computational and Molecular Population Genetics Lab, University of Bern
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Ecol. 2011 Apr;20(7):1450-62. doi: 10.1111/j.1365-294X.2011.05015.x.
Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis).
Fischer MC, Foll M, Excoffier L, Heckel G.
:: DESCRIPTION
SnIPRE (Selection Inference using a Poisson Random Effects model) is a new methodology for identifying genes under natural selection.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Comput Biol. 2012;8(12):e1002806. doi: 10.1371/journal.pcbi.1002806. Epub 2012 Dec 6.
SnIPRE: selection inference using a Poisson random effects model.
Eilertson KE1, Booth JG, Bustamante CD.
:: DESCRIPTION
SNPGenie is a program to estimate evolutionary parameters from pooled next-generation sequencing (NGS) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.
Nelson CW, Moncla LH, Hughes AL.
Bioinformatics. 2015 Jul 29. pii: btv449.
:: DESCRIPTION
Is It Chance is a very simple little program that demonstrates the power of natural selection to accumulate favorable variations is anything but “mere chance.”.Is It Chance pits chance and selection against each other in a race to match a string of random letters to a sentence typed in by the user, and reveals clearly the difference between natural selection and “mere chance.”
::DEVELOPER
The Queller/Strassmann Research Group at Washington University in St. Louis
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ADAPTSITE is a method of detecting positive and negative selection at single codon sites.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Suzuki Y. and Gojobori T. (1999)
A method for detecting positive selection at single amino acid sites.
Mol. Biol. Evol. 16:1315-1328.
