:: DESCRIPTION
imappingfamily is a package with a graphical interface regrouping the different methods presented in the article submitted “Quantitative Trait Locus Detection in a population with family structure”.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rabier C-E, Azais J-M, Elsen J-M, Delmas C.
Quantitative Trait Locus Detection in a population with family structure
(submitted)
:: DESCRIPTION
SENDBS computes average nucleotide substitutions within and between populations with standard errors of average nucleotide substitutions estimated with a bootstrap method by resampling sites. Also constructs a population tree with a neighbor-joining method.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Mol Biol Evol. 1989 May;6(3):290-300.
Variances of the average numbers of nucleotide substitutions within and between populations.
Nei M, Jin L.
:: DESCRIPTION
WhichRun is a computer program for population assignment of individuals based on multilocus genotype data.
::DEVELOPER
Michael A. Banks and Will Eichert @ MFGL
BODEGA MARINE LABORATORY ,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Banks, M.A. and W. Eichert. 2000.
WHICHRUN (Version 3.2) a computer program for population assignment of individuals based on multilocus genotype data.
Journal of Heredity. 91:87-89.
:: DESCRIPTION
StreamTree estimates how much each section of a river contributes to the genetic differentiation among populations.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalinowski ST, MH Meeuwig, SR Narum, ML Taper (2008)
Stream trees: a statistical method for mapping genetic differences between populations of freshwater organisms to the sections of streams that connect them.
Canadian Journal of Fisheries and Aquatic Sciences (65:2752-2760).
:: DESCRIPTION
MM-DIST is a computer program that calculates probability distributions for how many loci individuals in a population will differ by. For example, the graph below shows the probability of two individuals differing (mismatching) by 0 to 10 loci for unrelated individuals (solid line) and full siblings (dashed line) in a population of bighorn sheep.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalinowski ST, M Sawaya, ML Taper (2006)
Individual identification and distributions of genotypic differences.
Journal of Wildlife Management 70:148-150.
:: DESCRIPTION
Margarita infers genealogies from population genotype data and uses these to map disease loci.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mapping trait loci by use of inferred ancestral recombination graphs.
Minichiello MJ and Durbin R
American journal of human genetics2006;79;5;910-22
:: DESCRIPTION
ROADTRIPS is a C program that performs single-SNP, case-control association testing in samples with partially or completely unknown population and pedigree structure.ROADTRIPS uses an empirical covariance matrix calculated from genomewide SNP data to correct for unknown population and pedigree structure, while maintaining high power by taking advantage of known pedigree information when it is available. The program is applicable to association studies with completely general combinations of related and unrelated individuals. Analysis can be performed genomewide (currently just for autosomes).
::DEVELOPER
Timothy Thornton and Mary Sara McPeek
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Thornton T., McPeek M. S.
“ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure” (2010)
American Journal of Human Genetics, vol 86, pp. 172-184.
:: DESCRIPTION
Overpaint is a C++ package that can jointly estimate crossover rates, gene conversion rates and mean conversion tract lengths from population SNP dataset.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yin, J. Jordan, M. I., and Song, Y. S..
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data,
Bioinformatics, 25 (2009) i231-i239
:: DESCRIPTION
SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection. SelSim allows simulation from either a fully stochastic model of, or deterministic approximations to, natural selection within a coalescent framework. A number of different mutation models are available for simulating surrounding neutral variation. The package enables a detailed exploration of the effects of different models and strengths of selection on patterns of diversity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Spencer C., Coop, G. (2005)
SelSim: A program to simulate population genetic data with selection and recombination.
Bioinformatics. 2004 Dec 12;20(18):3673-5.
:: DESCRIPTION
TetraploidMap is a graphical user interface for calculating linkage maps for autotetraploid populations. It is suitable for handling markers scored on two parents and the full-sib offspring of a cross between them. TetraploidMap handles both codominant and dominant molecular markers, in all possible configurations, and takes into account the presence of null alleles in the analysis. It now includes a routine for QTL mapping.
::DEVELOPER
Christine Hackett at Biomathematics and Statistics Scotland (BioSS)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hackett, C.A.Milne, I., Bradshaw, J.E. & Luo, Z.W. 2007.
TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species.
Journal of Heredity 98, 727-729.
