GPA 0.9-3 – Genetic analysis incorporating Pleiotropy and Annotation

GPA 0.9-3

:: DESCRIPTION

GPA is a statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux/ Windows

:: DOWNLOAD

 GPA

:: MORE INFORMATION

Citation

GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation.
Chung D, Yang C, Li C, Gelernter J, Zhao H.
PLoS Genet. 2014 Nov 13;10(11):e1004787. doi: 10.1371/journal.pgen.1004787.

MORGAN 3.3 – Monte Carlo Genetic Analysis

MORGAN 3.3

:: DESCRIPTION

MORGAN (Monte Carlo Genetic Analysis) is a collection of programs and libraries developed at the University of Washington under the PANGAEA (Pedigree Analysis for Genetics and Epidemiological Attributes) umbrella. This software implements a number of methods for the analysis of data observed on members of a pedigree, with the main programs implementing Markov Chain Monte Carlo (MCMC) methods.

::DEVELOPER

Elizabeth A. Thompson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MORGAN 

:: MORE INFORMATION

Citation:

E. A. Thompson (1995)
Monte Carlo in Genetic Analysis.
Technical report No. 294, Department of Statistics, University of Washington.

E. A. Thompson (2000)
Statistical Inferences from Genetic Data on Pedigrees
NSF-CBMS Regional Conference Series in Probability and Statistics. Volume 6. IMS, Beachwood, OH.

CGEN 3.2.0 – Genetic Analysis of Case-Control Data

CGEN 3.2.0

:: DESCRIPTION

CGEN (Case-control.Genetics) is an R package for analyzing genetic data on case-control samples, with particular emphasis on novel methods for detecting Gene-Gene and Gene-Environment interactions.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  CGEN

:: MORE INFORMATION

Citation

Am J Hum Genet. 2010 Mar 12;86(3):331-42. doi: 10.1016/j.ajhg.2010.01.026. Epub 2010 Mar 4.
Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies.
Bhattacharjee S, Wang Z, Ciampa J, Kraft P, Chanock S, Yu K, Chatterjee N.

jPopGen 1.0b7 – Collection of Java programs for Population Genetic Analysis

jPopGen 1.0b7

:: DESCRIPTION

jPopGen Suite is an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences.

::DEVELOPER

Xiaoming Liu, Ph.D.(xmliu.uth{at}gmail.com)

:: SCREENSHOTS

jPopGen

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 jPopGen

:: MORE INFORMATION

Citation:

Methods Ecol Evol. 2012 Aug 1;3(4):624-627. Epub 2012 Mar 2.
jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.
Liu X.

mpMap 1.14 – Genetic Analysis of Multi-parent Recombinant Inbred Lines

mpMap 1.14

:: DESCRIPTION

mpMap is an R package for the genetic analysis of multi-parent recombinant inbred lines. It is a computational tool for complex experimental breeding designs. Careful attention has been paid to meeting the practical needs of potential users. Functions in the package encompass the full spectrum of analysis tasks: simulation, marker map construction, haplotype reconstruction and QTL mapping.

::DEVELOPER

CSIRO Mathematics, Informatics and Statistics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mpMap

:: MORE INFORMATION

Citation:

R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines.
Huang BE, George AW.
Bioinformatics. 2011 Mar 1;27(5):727-9.

BEAGLE 4 – Genetic Analysis Software Package

BEAGLE 4

:: DESCRIPTION

BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can

  • phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios.
  • infer sporadic missing genotype data.
  • impute ungenotyped markers that have been genotyped in a reference panel.
  • perform single marker and haplotypic association analysis.
  • detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BEAGLE

:: MORE INFORMATION

Citation:

B L Browning and S R Browning (2013)
Improving the accuracy and efficiency of identity by descent detection in population data.
Genetics 194(2):459-71. doi:10.1534/genetics.113.150029

B L Browning and S R Browning (2011)
A fast, powerful method for detecting identity by descent.
The American Journal of Human Genetics 88:173-182.

R/gap 1.1-3 – R/Genetic Analysis Package

R/gap 1.1-3

:: DESCRIPTION

R/gap (R/Genetic Analysis Package) is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

::DEVELOPER

Jing Hua Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 R/gap

:: MORE INFORMATION

Molkin 3.0 – Genetic analysis of Populations using Molecular Coancestry Information

Molkin 3.0

:: DESCRIPTION

MolKin is a population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. Primary functions carried out by MolKin are the computation of the between individuals (and populations) molecular coancestry coefficients (fij), the Kinship distance (Dk) at individual and population levels. Additionally, users can compute with MolKin a set of among populations, genetic distances and F-statistics (Wright, 1978) from multilocus information. The current version of MolKin provides different methods to quantify contributions to diversity to set priorities for conservation. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation.

::DEVELOPER

Juan Pablo Gutiérrez García

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Molkin

:: MORE INFORMATION

Citation:

Gutierrez, Royo, Alvarez, Goyache (2005),
Molkin v2.0: a computer program for genetic analysis of populations using molecular coancestry information“,
Journal of Heredity, 96:718-721.