LIBFBAT 0.5.1 – C++ library for Family Based Association Testing

LIBFBAT 0.5.1

:: DESCRIPTION

LIBFBAT programming library s robust both to genotyping errors and missing genotypes. The underlying method consists in considering an incomplete data model where the true unobserved genotypes produce the observed one through an explicit genotyping error model.

::DEVELOPER

LIBFBAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Mac OsX/ Linux
C++ Compiler

:: DOWNLOAD

LIBFBAT

:: MORE INFORMATION

Citation

Gregory Nuel, Yousri Slaoui and Vincent Miele,
libfbat: a C++ library for family based association testing,
Proceedings of JOBIM, 2008

3FunMap 1.0 – Full-sib Family Functional Mapping tools

3FunMap 1.0

:: DESCRIPTION

3FunMap is a Windows software that can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, the software utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating local ordering methods. Multi-locus linkage phases for the optimal order of each linkage group are predicted based on three-point linkage analysis.

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

3FunMap

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2006-8. doi: 10.1093/bioinformatics/btr306. Epub 2011 May 17.
3FunMap: full-sib family functional mapping of dynamic traits.
Tong C, Wang Z, Zhang B, Shi J, Wu R.

EcMap – Evaluate the size of Families for Linkage analysis

EcMap

:: DESCRIPTION

EcMap is a simulation program that allows users to evaluate the size of their families for linkage analysis. The software simulates homologous recombination and inheritance process based on a Chi-square model simulating physical interference but not chromatid interference. The genetic distance map was obtained from HapMap and reflects average male and female genetic distances for each chromosome

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

EcMap

:: MORE INFORMATION

PEDDY v0.4.3 – Detect Sample Mixups in Family based studies of Disease

PEDDY v0.4.3

:: DESCRIPTION

PEDDY is a software package to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

PEDDY

:: MORE INFORMATION

Citation:

Am J Hum Genet. 2017 Mar 2;100(3):406-413. doi: 10.1016/j.ajhg.2017.01.017. Epub 2017 Feb 9.
Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.
Pedersen BS, Quinlan AR.

GCORE 201510 – Fast Family-based Gene-gene Interaction Test

GCORE 201510

:: DESCRIPTION

GCORE is an efficient family-based gene-gene interaction test for trios.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GSCORE

:: MORE INFORMATION

Citation

An efficient gene-gene interaction test for genome-wide association studies in trio families.
Sung PY, Wang YT, Yu YW, Chung RH.
Bioinformatics. 2016 Feb 11. pii: btw077.

OPTPDT – Family-based multi-SNP Association Test

OPTPDT

:: DESCRIPTION

OPTPDT (Optimal P-value Threshold Pedigree Disequilibrium Test)is a family-based multi-SNP association test. A variable p-value threshold algorithm is used in the test to select an optimal subset of SNPs that has the strongest association signals.

::DEVELOPER

Statistical Genetics and Programming Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

OPTPDT

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 15;16:381. doi: 10.1186/s12864-015-1620-3.
A multi-SNP association test for complex diseases incorporating an optimal P-value threshold algorithm in nuclear families.
Wang YT, Sung PY, Lin PL, Yu YW, Chung RH

CMCompare 0.0.1 – Discriminatory Power of RNA Family Models

CMCompare 0.0.1

:: DESCRIPTION

The CMCompare program takes two Infernal covariance models and calculates the Link sequence and its Link score. The Link sequence is the sequence scored by both models highest at the same time. Two models with a high Link score are not well separated from each other.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CMCompare

:: MORE INFORMATION

Citation

Discriminatory power of RNA family models
Höner zu Siederdissen, Christian and Hofacker, Ivo L.
Bioinformatics, 2010, 26, 453-459

KING 1.4 – Identify Family and Population Structure

KING 1.4

:: DESCRIPTION

KING (Kinship-based INference for Gwas) is a toolset for identifing family and population structure using genome-wide SNP data. KING can be used to check family relationship and flag pedigree errors by estimating all kinship coefficients for all pairwise relationships. Unrelated pairs can be well separated from close relatives (up to 3rd-degree) and vice versa.

::DEVELOPER

Wei-Min Chen

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

KING

:: MORE INFORMATION

Citation

Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010)
Robust relationship inference in genome-wide association studies.
Bioinformatics 26(22):2867-2873