Tag: Individual

AncestryPainter v5 – Illuminate the Ancestry Compositions of Populations and Individuals

AncestryPainter v5

:: DESCRIPTION

AncestryPainter is a graphic program used to illuminate the ancestry compositions of populations and individuals in a way to save space with a rounded and nice-looking graph.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

AncestryPainter

:: MORE INFORMATION

Citation

Feng Q, Lu D, Xu S.
AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals.
Genomics Proteomics Bioinformatics. 2018 Oct;16(5):382-385. doi: 10.1016/j.gpb.2018.05.002. Epub 2018 Nov 22. PMID: 30472416; PMCID: PMC6364040.

DeNovoGear 1.1.1 – Detect denovo Mutations using Sequencing data of Related Individuals

DeNovoGear 1.1.1

:: DESCRIPTION

DeNovoGear is a program to detect denovo mutations using sequencing data.

::DEVELOPER

The Cartwright Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • C Compiler

:: DOWNLOAD

 DeNovoGear

:: MORE INFORMATION

Citation

Donald F Conrad et al.
Variation in genome-wide mutation rates within and between human families
Nature Genetics 43, 712–714 (2011) doi:10.1038/ng.862

SGS v2 – Analysis of Spatial Genetic and Phenotypic Structures of Individuals and Population

SGS v2

:: DESCRIPTION

SGS (Spatial Genetic Software) is a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations

::DEVELOPER

Bernd Degen

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SGS

:: MORE INFORMATION

Citation

Degen, Petit, Kremer (2001),
“SGS – Spatial Genetic Software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations”,
Journal of Heredity, 92(5):447-448.

MQLS 1.5 – Case-Control Association Testing with Related Individuals

MQLS 1.5

:: DESCRIPTION

MQLS (More Powerful Quasi-Likelihood Score Test)can handle arbitrary number of markers and samples and have other features that we found useful in our studies, such as pedigree checking and input/output formats. In addition to genotyped markers, this version can carry out association tests using imputed allele counts (“dosages”) generated by MACH and an empirical variance estimator.

::DEVELOPER

Liming Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

  MQLS

:: MORE INFORMATION

Reference

Thornton T., McPeek M. S. (2007)
Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test.
Am J Hum Genet, 81, 321-337.

FEstim 1.3.2 – Estimation of the Inbreeding Coefficient of Individuals

FEstim 1.3.2

:: DESCRIPTION

FEstim is a software for estimation of the inbreeding coefficient of individuals through use of a dense map of genetic markers and computation of genomically controlled homozygosity mapping lodscores.

::DEVELOPER

FEstim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

 FEstim

:: MORE INFORMATION

Citation

Am J Hum Genet. 2006 Jul;79(1):62-6. Epub 2006 Apr 28.
Using genomic inbreeding coefficient estimates for homozygosity mapping of rare recessive traits: application to Taybi-Linder syndrome.
Leutenegger AL, Labalme A, Genin E, Toutain A, Steichen E, Clerget-Darpoux F, Edery P.

Syzygy 1.2.7 – SNP and Indel Calling for pooled and individual Targeted Resequencing Studies

Syzygy 1.2.7

:: DESCRIPTION

Syzygy is a targeted sequencing post processing analysis tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant.

::DEVELOPER

Rivas Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Syzygy

:: MORE INFORMATION

Citation

Rivas et al. (2011),
“Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease“,
Nature Genetics 43, 1066–1073 (2011)

rarefy 1.0 – Selecting Informative Individuals and Families in a Sample

rarefy 1.0

:: DESCRIPTION

Rarefy is a C++ tool to facilitate sequencing study design using family samples by selecting informative families and individuals from a sample. It takes account pedigree structure and calculates an informative score for each individual to evaluate the potential of carrying trait-influencing rare variants. Rarefy has been used for selecting individuals in Minnesota Twins substance abuse whole-genome sequencing project and SardiNia deep sequencing project.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 Rarefy

:: MORE INFORMATION

hindex 1.42 – Calculates a Hybrid Index for Individuals of unknown Ancestry

hindex 1.42

:: DESCRIPTION

hindex calculates a hybrid index for individuals of unknown ancestry. The index is based on information from molecular markers and uses maximum-likelihood to estimate the proportion of alleles that were inherited from one of two hybridizing parental species.

::DEVELOPER

Buerkle lab ,University of Wyoming

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 hindex

:: MORE INFORMATION

Citation:

Buerkle, C. Alex. 2005.
Maximum-likelihood estimation of a hybrid index based on molecular markers.
Molecular Ecology Notes 5: 684-687

RelCheck 0.67 – Verify Relationships between all pairs of Individuals

RelCheck 0.67

:: DESCRIPTION

RelCheck is a software for verifying relationships between all pairs of individuals in a linkage study

::DEVELOPER

Karl W Broman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RelCheck

:: MORE INFORMATION

Citation

Broman, Weber (1998),
“Estimation of pairwise relationships in the presence of genotyping errors” (letter),
American Journal of Human Genetics, 63(5):1563-1564.

WhichRun 4.1 – software for Assigning Individuals to Populations

WhichRun 4.1

:: DESCRIPTION

WhichRun is a computer program for population assignment of individuals based on multilocus genotype data.

::DEVELOPER

Michael A. Banks and Will Eichert  @ MFGL
BODEGA MARINE LABORATORY ,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 WhichRun 

:: MORE INFORMATION

Citation:

Banks, M.A. and W. Eichert. 2000.
WHICHRUN (Version 3.2) a computer program for population assignment of individuals based on multilocus genotype data.
Journal of Heredity. 91:87-89.