:: DESCRIPTION
MSS (Maximal Segmental Score) is an R program for the analysis of genome-wide association data
::DEVELOPER
Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Using maximal segmental score in genome-wide association studies.
Lin YC, Hsiao CL, Hsieh AR, Lian IeB, Fann CS.
Genet Epidemiol. 2012 Sep;36(6):594-601. doi: 10.1002/gepi.21652.
:: DESCRIPTION
MicroFamily is a program designed for identifying flanking region similarities between different microsatellite sequences obtained from screening partial genomic libraries.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Meglécz, E. 2007.
MicroFamily: A computer program for detecting flanking region similarities among different microsatellite loci.
Molecular Ecology Notes 7 : 18-20
:: DESCRIPTION
GP and Arka are very leightweighed programs for manipulation of DNA / RNA / protein sequences. They are designed on one hand to run smoothly on older machines, and on the other — to faciliate processing of large numbers of sequence / data files. GP includes utilities to convert DNA / RNA to protein, determine codon usage / GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Ped-sim enables simulations of data for individuals from a given pedigree structure. It can use sex-specific genetic maps to incorporate differences in male and female recombination events.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Caballero M, Seidman DN, Qiao Y, Sannerud J, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Carmi S, Williams AL.
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.
PLoS Genet. 2019 Dec 20;15(12):e1007979. doi: 10.1371/journal.pgen.1007979. PMID: 31860654; PMCID: PMC6944377.
:: DESCRIPTION
Hapi is a program that efficiently infers minimum recombinant and maximum likelihood haplotypes for nuclear families.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2010;11(10):R108. doi: 10.1186/gb-2010-11-10-r108. Epub 2010 Oct 29.
Rapid haplotype inference for nuclear families.
Williams AL, Housman DE, Rinard MC, Gifford DK.
:: DESCRIPTION
SPLATCHE (for SPatiaL And Temporal Coalescences in Heterogenous Environment) is a program that allows to incorporate the influence of environment in the simulation of migration of a given species from one origin. In a second phase, the molecular genetic diversity of one or several samples drawn from the simulated species can be generated.
::DEVELOPER
Computational and Molecular Population Genetics Lab, University of Bern
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N.
SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.
Bioinformatics. 2019 Nov 1;35(21):4480-4483. doi: 10.1093/bioinformatics/btz311. PMID: 31077292; PMCID: PMC6821363.
Ray N, Currat M, Foll M, Excoffier L. (2010)
SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination.
Bioinformatics, Volume 26, Issue 3, Page 2993-2994.
:: DESCRIPTION
The package CodABC is computer framework to coestimate Recombination, Substitution and Molecular Adaptation (dN/dS) rates by approximate Bayesian computation from coding sequence alignments.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.
CodABC: A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.
Arenas M, Lopes JS, Beaumont MA, Posada D
:: DESCRIPTION
RUNTC is an estimator of first coalescent time, which is the time when a copy of a gene most recently shared ancestry with other copies of that gene. This is also an estimate of the upper bound of when a mutation has arisen, and it can be used to study the ages of alleles that are found in a population.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Platt A, Pivirotto A, Knoblauch J, Hey J.
An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations.
PLoS Genet. 2019 Aug 19;15(8):e1008340. doi: 10.1371/journal.pgen.1008340. PMID: 31425500; PMCID: PMC6715256.
:: 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
IMa2 (Isolation with Migration) implements a method for generating posterior probabilities for complex demographic population genetic models. IMa2 can handle data and implement a model for multiple populations (for numbers of sampled populations between one and ten) – not just two populations (as was the case with the original IM and IMa programs).
IMa3 is the newest in the IM sequence of programs. It can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hey J, Nielsen R. 2007.
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics.
Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2785-90.
