MAPDISTO 1.8.1 – Map Genetic Markers in Experimental Segregating Populations Like Backcross

MAPDISTO 1.8.1

:: DESCRIPTION

MAPDISTO is a program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes.

::DEVELOPER

Mathias Lorieux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Excel

:: DOWNLOAD

 MAPDISTO

:: MORE INFORMATION

Citation:

Lorieux M (2012)
MapDisto: fast and efficient computation of genetic linkage maps.
Molecular Breeding, August 2012, Volume 30, Issue 2, pp 1231-1235

infocalc 1.1 – Measure the Ancestry Information Content of Genetic Markers

infocalc 1.1

:: DESCRIPTION

infocalc is a small script for calculating statistics that measure the ancestry information content of genetic markers.

::DEVELOPER

Rosenberg lab at Stanford University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

  infocalc

:: MORE INFORMATION

Citation

Informativeness of genetic markers for inference of ancestry.
Rosenberg NA, Li LM, Ward R, Pritchard JK.
Am J Hum Genet. 2003 Dec;73(6):1402-22. Epub 2003 Nov 20.

MAGMA 1.1 – Multiobjective Analyzer for Genetic Marker Acquisition

MAGMA 1.1

:: DESCRIPTION

MAGMA employs a multiobjective evolutionary algorithm to pick tag SNPs from a larger set of SNPs while balancing multiple objectives (e.g., cost and sensitivity).

::DEVELOPER

Family Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MAGMA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2003 Jul 23;4:30. Epub 2003 Jul 23.
Evolutionary algorithms for the selection of single nucleotide polymorphisms.
Hubley RM, Zitzler E, Roach JC.

wclique 0.1 – Genetic Marker Selection program

wclique 0.1

:: DESCRIPTION

wclique is a C++ program that helps select genetic or RH markers for framework mapping.

::DEVELOPER

Humberto Ortiz Zuazaga

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • C++ Compiler

:: DOWNLOAD

  wclique

:: MORE INFORMATION

PowerMarker 3.25 – Statistical Software for Genetic Marker data analysis

PowerMarker 3.25

:: DESCRIPTION

PowerMarker is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis.

::DEVELOPER

Jack Liu powermarker@hotmail.com

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PowerMarker

:: MORE INFORMATION

Citation

Bioinformatics. 2005 May 1;21(9):2128-9. Epub 2005 Feb 10.
PowerMarker: an integrated analysis environment for genetic marker analysis.
Liu K, Muse SV.

EPISTACY 2.0 – Detect Two-locus Epistatic Interactions using Genetic Marker information

EPISTACY 2.0

:: DESCRIPTION

EPISTACY is a SAS program designed to test all possible two-locus combinations for epistatic (interaction) effects on a quantitative trait using QTL-mapping data sets.

::DEVELOPER

Dr Jim Holland 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 EPISTACY

:: MORE INFORMATION

Citation

Holland (1998),
EPISTACY: A SAS program for detecting two-locus epistatic interactions using genetic marker information“,
Journal of Heredity, 89:374-375.

RELPAIR 2.0.1 – Relationship of Pairs of Individuals based on Genetic Marker Data

RELPAIR 2.0.1

:: DESCRIPTION

RELPAIR  is a FORTRAN 77 program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample.

::DEVELOPER

the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • FORTRAN

:: DOWNLOAD

 RELPAIR

:: MORE INFORMATION

Citation

Epstein, M.P., Duren, W.L., and Boehnke, M. (2000)
Improved inference of relationships for pairs of individuals.
American Journal of Human Genetics 67:1219-1231.

LCMT – Multiple Genetic Markers Association test

LCMT

:: DESCRIPTION

LCMT is a small program performing “combining” association test over multiple genetic markers.LCMT implements the “combining” method for the association test over multiple genetic markers. It optimally utilizes the information from those markers. It is preferred over several competing tests, such as the Bonferroni procedure, the permutation procedure, the traditional χ2 procedure, the regression procedure (Hotelling T2 test) and the haplotype-based test.

::DEVELOPER

FBAT-Toolkit Team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux/ Sunsparc stations

:: DOWNLOAD

LCMT

:: MORE INFORMATION

References

H zhou, L wei, X Xu, X Xu (2006) Combining association tests across multiple genetic markers in case-control studies