GRR 1.2.1.41 – Detect Pedigree Errors

GRR 1.2.1.41

:: DESCRIPTION

GRR (Graphical Representation of Relationships) is a Windows-based application for detecting pedigree errors via graphically inspecting the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GRR

:: MORE INFORMATION

If you decide to use GRR, please take a minute to register.

MERLIN 1.1.2 – Pedigree Analysis

MERLIN 1.1.2

:: DESCRIPTION

MERLIN (multipoint engine for rapid likelihood inference ) uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around. it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

MERLIN

:: MORE INFORMATION

Citation:

Abecasis GR, Cherny SS, Cookson WO and Cardon LR
Merlin-rapid analysis of dense genetic maps using sparse gene flow trees.
Nat Genet (2002) 30:97-101

If you decide to useMERLIN, please take a minute to register.

PEDSTATS 0.6.12 – Statistics & Quality Assessments for Gene-mapping Data

PEDSTATS 0.6.12

:: DESCRIPTION

PEDSTATS is a handy tool for quick validation and summary of any pair of pedigree (.ped) and data (.dat) files.PEDSTATS produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

PEDSTATS

:: MORE INFORMATION

Citation:

Wigginton JE and Abecasis GR (2005)
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data
Bioinformatics 21:3445 – 3447.

If you decide to use PEDSTATS, please take a minute to register.

LAMP 0.0.12 – Linkage & Association Modeling for Pedigrees

LAMP 0.0.12

:: DESCRIPTION

LAMP (Linkage & Association Modeling for Pedigrees) uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

LAMP

:: MORE INFORMATION

Citation:

Li, Boehnke and Abecasis (2005).
Joint Modeling of Linkage and Association: Identifying SNPs Responsible for a Linkage
Signal. Am J Hum Genet 76:934-49

Li, Boehnke and Abecasis (2006).
Efficient study designs for test of genetic association using sibship data and unrelated cases and controls.
Am J Hum Genet 78:778-92

GIGI-Pick 1.06 – Subject Selection for Sequencing in Pedigrees

GIGI-Pick 1.06

:: DESCRIPTION

GIGI-Pick is a computer program that facilitates the evaluation and comparison of subject selection choices in sequencing studies in pedigrees.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GIGI-Pick

:: MORE INFORMATION

Citation:

Cheung CYK, Blue EM, Wijsman EM (2014)
A statistical framework to guide sequencing choices in pedigrees.
American Journal of Human Genetics 94:257-267.

PedCut 1.19 – Cutting large and complex Pedigrees for Linkage Analysis

PedCut 1.19

:: DESCRIPTION

PedCut is a program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size

::DEVELOPER

Group of the Methods of Genetic Analysis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PedCut

:: MORE INFORMATION

Citation:

Eur J Hum Genet. 2008 Jul;16(7):854-60. doi: 10.1038/ejhg.2008.24. Epub 2008 Feb 27.
An approach for cutting large and complex pedigrees for linkage analysis.
Liu F, Kirichenko A, Axenovich TI, van Duijn CM, Aulchenko YS.

reHCstar 2.1.3 – Algorithm for Haplotype Inference problem on Pedigree data with Recombinations, Errors and Mutations

reHCstar 2.1.3

:: DESCRIPTION

reHCstar is a SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • CMake
  • GNU make
  • Boost FileSystem, System, DateTime, ProgramOptions, IOStreams, and other include-only libraries
  • Apache Log4cxx

:: DOWNLOAD

 reHCstar

:: MORE INFORMATION

Citation

Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, and Paola Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012).

PedVizApi 0.15 – Visual Analysis of large and complex Pedigrees

PedVizApi 0.15

:: DESCRIPTION

PedVizApi is a Java Api for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data.

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 PedVizApi

:: MORE INFORMATION

Citation

Fuchsberger, Falchi, Forer, Pramstaller (2007),
PedVizApi: A Java API for the interactive, visual analysis of extended pedigrees“,
Bioinformatics, 24(2):279-281

PRIMUS 1.8.0 – Pedigree Reconstruction and Identification of a Maximum Unrelated Set

PRIMUS 1.8.0

:: DESCRIPTION

PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data.

::DEVELOPER

PRIMUS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PRIMUS

:: MORE INFORMATION

Citation

PRIMUS: Improving Pedigree Reconstruction using Mitochondrial and Y Haplotypes.
Staples J, Ekunwe L, Lange E, Wilson JG, Nickerson DA, Below JE.
Bioinformatics. 2015 Oct 29. pii: btv618

GenomeLaser – Haplotyping from Pedigree Genotypes

GenomeLaser 1.5

:: DESCRIPTION

GenomeLaser is a tool for haplotype inference from pedigree genotypes.

::DEVELOPER

GenomeLaser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GenomeLaser

:: MORE INFORMATION

Citation

GenomeLaser: fast and accurate haplotyping from pedigree genotypes.
Li W, Fu G, Rao W, Xu W, Ma L, Guo S, Song Q.
Bioinformatics. 2015 Aug 18. pii: btv452.