LINKAGE – Pedigree Linkage Analysis

LINKAGE

:: DESCRIPTION

LINKAGE package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three-generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.

::DEVELOPER

Lab of Statistical Genetics, Rockefeller University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

LINKAGE

:: MORE INFORMATION

Pseudomarker 2.0 – Joint Linkage / Linkage Disequilibrium Analysis

Pseudomarker 2.0

:: DESCRIPTION

PSEUDOMARKER is linkage analysis software for joint Linkage and LD analysis for qualitative traits. Pseudomarker can analyze different data structures jointly such as cases and controls, trios, sib pairs, sib ships and extended families. Pseudomarker is family-based association test.

::DEVELOPER

Tero Hiekkalinna , Joseph D. Terwilliger and Petri Norrgrann.

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD AUTOSCAN

Pseudomarker

:: MORE INFORMATION

Citaiton

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD.
Gertz EM, Hiekkalinna T, Digabel SL, Audet C, Terwilliger JD, Schäffer AA.
BMC Bioinformatics. 2014 Feb 17;15:47. doi: 10.1186/1471-2105-15-47.

Harald H. H. Göring and Joseph D. Terwilliger
Linkage Analysis in the Presence of Errors IV: Joint Pseudomarker Analysis of Linkage and/or Linkage Disequilibrium on a Mixture of Pedigrees and Singletons When the Mode of Inheritance Cannot Be Accurately Specified.
American Journal of Human Genetics 66:1310-1327, 2000

APL 1.1 – Association in the Presence of Linkage

APL 1.1

:: DESCRIPTION

APL (Association in the Presence of Linkage) provides a novel test for association in the presence of linkage using general pedigree data.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

APL

:: MORE INFORMATION

Citation

Chung R-H, Hauser ER, Martin ER (2006)
The APL test: Extension to general nuclear families and haplotypes and examination of its robustness.
Human Heredity. 61(4):189-99.

SIMLA 3.3 – SIMulation of Pedigree Data for Linkage and Association Studies

SIMLA 3.3

:: DESCRIPTION

SIMLA (SIMulation of pedigree data for Linkage and Association studies) is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows
Java

:: DOWNLOAD

SIMLA

:: MORE INFORMATION

Citation

Schmidt MA, Hauser ER, Martin ER, Schmidt S.
Extension of the SIMLA package for gener ating pedigrees with complex inheritance patterns: Environmental covariates, gene-gene and gene-environment interaction.
Stat Appl Genet Mol Biol 4(1): article 15, 2005.

COCACOLA – Binning Metagenomic Contigs using Sequence COmposition, Read CoverAge, CO-alignment, and Paired-end Read LinkAge

COCACOLA

:: DESCRIPTION

COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
MatLab

:: DOWNLOAD

COCACOLA

:: MORE INFORMATION

Citation

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge.
Lu YY, Chen T, Fuhrman JA, Sun F.
Bioinformatics. 2016 Jun 2. pii: btw290.

LDlink / LDlinkR 1.1.2 – Linkage Disequilibrium in Population group

LDlink / LDlinkR 1.1.2

:: DESCRIPTION

LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.

LDhap: Calculate population specific haplotype frequencies of all haplotypes observed for a list of query SNPs. Input is a list of SNP RS numbers (one per line) and a population group.

LDmatrix: Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics. Input is a list of SNP RS numbers (one per line) and a population group.

LDpair: Investigate correlated alleles for a pair of SNPs in high LD. Input is two RS numbers and a population group.

LDproxy: Interactively explore proxy and putatively functional SNPs for a query SNP. Input is an RS number and a population group.

::DEVELOPER

Mitchell Machiela in collaboration with NCI’s Center for Biomedical Informatics and Information Technology (CBIIT).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser
R

:: DOWNLOAD

LDlinkR

:: MORE INFORMATION

Citation

LDlink: A web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.
Machiela MJ, Chanock SJ.
Bioinformatics. 2015 Jul 2. pii: btv402.

lnkg2lmlnk 20120312 / lnkg2lmm 20070901 – Converter from Linkage-style to Morgan ver 3 style data files

lnkg2lmlnk 20120312 / lnkg2lmm 20070901

:: DESCRIPTION

lnkg2lmlnk is a new converter from Linkage-style to Morgan ver 3 style data files

lnkg2lmm is a Perl script to convert linkage-style files to MORGAN-lm_markers-style files.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

lnkg2lmlnk / lnkg2lmm

:: MORE INFORMATION

Citation:

Am J Hum Genet. 2006 Nov;79(5):846-58. Epub 2006 Sep 20.
Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain-Monte Carlo provides practical approaches for genome scans on general pedigrees.
Wijsman EM1, Rothstein JH, Thompson EA.

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

Linkdatagen 20130704 – Generates LINKAGE Style Files

Linkdatagen 20130704

:: DESCRIPTION

Linkdatagen is a PERL script that generates LINKAGE style files for ALLEGRO , MERLIN, PREST, MORGAN, PLINK, FEstim, BEAGLE and RELATE using as input genotype calls from Affymetrix SNP chips, Illumina SNP chips, or SNP genotypes inferred from massively parallel sequencing (MPS) data, such as whole exome or whole genome sequence data.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Windows / Linux / MacOsX
Perl

:: DOWNLOAD

Linkdatagen

:: MORE INFORMATION

Citation

Bahlo M, Bromhead CJ (2009).
Generating linkage mapping files from Affymetrix SNP chip data.
Bioinformatics 25(15):1961-2.

fastlink 4.1P – Improved Version of LINKAGE

fastlink 4.1P

:: DESCRIPTION

FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation.

::DEVELOPER

Alejandro Schäffer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

FASTLINK

:: MORE INFORMATION

Citation:

Cottingham Jr. RW, Idury RM, Schäaffer AA:
Faster Sequential Genetic Linkage Computations.
American Journal of Human Genetics 53:252-263, 1993.

Schäffer AA, Gupta SK, Shriram K, Cottingham Jr. RW:
Avoiding Recomputation in Linkage Analysis.
Human Heredity 44:225-237, 1994.