LAMP 2.5 / LAMP-LD 1.1 – Estimate Locus Specific Ancestry

LAMP 2.5 / LAMP-LD 1.1

:: DESCRIPTION

LAMP (Local Ancestry in adMixed Populations) is a software for the inference of locus-specific ancestry in recently admixed populations. LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote.

LAMP-LD is a software package for the inference of locus-specific ancestry in recently admixed populations.

::DEVELOPER

Computational Genetics Group

:: REQUIREMENTS

Linux

:: DOWNLOAD

LAMP / LAMP-LD

:: MORE INFORMATION

Citation:

Sriram Sankararaman, Srinath Sridhar, Gad Kimmel and Eran Halperin,
Estimating Local Ancestry in Admixed Populations,
The American Journal of Human Genetics, Volume 82, Issue 2, 290-303, 2008.

Bioinformatics. 2012 May 15;28(10):1359-67. doi: 10.1093/bioinformatics/bts144. Epub 2012 Apr 11.
Fast and accurate inference of local ancestry in Latino populations.
Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Burchard EG, Halperin E.

GLAPD – Whole Genome based LAMP Primer Design for a set of Target Genome

GLAPD

:: DESCRIPTION

GLAPD can design LAMPP(Loop-mediated isothermal amplification) primer sets based on a whole genome. It can also design LAMP primers for a set of target genomes. Users can specify a group of background genomes.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Bowtie
CUDA driver

:: DOWNLOAD

GLAPD

:: MORE INFORMATION

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