Category: Genetics & Pedigree

LocusView 2.0 – Generate Images of Chromosomal Regions

LocusView 2.0

:: DESCRIPTION

LocusView is a program for generating images of chromosomal regions annotated with genomic features, experimental data, and analysis results.

:DEVELOPER

Tracey Petryshen, Andrew Kirby, and Mark Ainscow , The Broad Institute, Cambridge, MA

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX
  • Java

:: DOWNLOAD

LocusView

:: MORE INFORMATION

Citation

Please cite “T. Petryshen, A. Kirby, M. Ainscow, unpublished software” when using LocusView in publications

If you aren’t already registered, please send an email to locusview@broadinstitute.orgwith your name and email address, so that we can update you on new releases, bug fixes, etc.

 

DISTANCE – Plot Genetic Distances between Populations

DISTANCE

:: DESCRIPTION

DISTANCE uses an evolutionary algorithm to find suitable placings on a 2-dimensional surface. Genetic distances between populations (or between individuals) are supplied in your text file.

::DEVELOPER

Brian  Kinghorn.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DISTANCE

:: MORE INFORMATION

Citation

Kinghorn, B.P. and Shepherd, R.K. 2001.
A graphic display of genetic distances between populations.
Assoc. Advmt. Anim. Breed. Genet. 14: 273-276.

PEDIGREE VIEWER 6.5b – Draw & Manipulate Pedigree Diagrams

PEDIGREE VIEWER 6.5b

:: DESCRIPTION

PEDIGREE VIEWER reads your simple data file and displays the full pedigree structure on the screen. Each animal is represented by its identity, or its name, or by its value for any of the traits in the data file. You can display a large pedigree of thousands of animals all on the screen at the one time. Data are overlapped on the screen for such large pedigrees, but in one mode an individual’s information is highlighted as the mouse cursor passes over. You can ask to find an animal(s) by identity, or by merit or merit range for a given trait.

::DEVELOPER

by Brian and Sandy Kinghorn.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PEDIGREE VIEWER

:: MORE INFORMATION

Citation

Brian P Kinghorn
An algorithm for efficient constrained mate selection
Genetics Selection Evolution 2011, 43:4

GEST98 – Analysis of Genotype x Environment Interaction

GEST98

:: DESCRIPTION

GEST98 is a computer package for the analysis of  genotype x environment interaction  of a quantitative trait.

::DEVELOPER

Yasuo UKAI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GEST98

:: MORE INFORMATION

When you publish a paper including results which were obtained by utilizing Gest, then please put a short sentence in your paper telling that “Gest98 was used.” .

MAPL98 – Linkage Mapping & QTL Analysis

MAPL98

:: DESCRIPTION

MAPL98 is a software for constructing  detailed linkage maps of organisms and analysis of quantitative trait loci(QTLs) and can be run on a personal computer which will be available in an  ordinal laboratory. It provides experimenter freindly computer environment.

::DEVELOPER

Yasuo UKAI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MAPL98

:: MORE INFORMATION

When you publish a paper including results which were obtained by utilizing Mapl, then please put a short sentence in your paper telling that “Mapl98 was used.” .

Metal 20110325 – Meta-analysis of Genomewide Association Scans

Metal 20110325

:: DESCRIPTION

Metal (Meta Analysis Helper) is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Metal

:: MORE INFORMATION

Citation:

Cristen J. Willer, Yun Li and Gonçalo R. Abecasis
METAL: fast and efficient meta-analysis of genomewide association scans
Bioinformatics (2010) 26 (17): 2190-2191.

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

SimWalk 2.91 – Statistical Analysis of Qualitative Traits

SimWalk 2.91

:: DESCRIPTION

SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.

::DEVELOPER

Eric Sobel (simwalk@genetics.ucla.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

SimWalk

:: MORE INFORMATION

Citation:

Sobel E, Papp JC, Lange K (2002)
Detection and integration of genotyping errors in statistical genetics.
American Journal of Human Genetics 70:496-508.

GeneSeq 1.0 – LD-based Genotype Calling from Shotgun Sequencing Reads

GeneSeq 1.0

:: DESCRIPTION

GeneSeq package provides methods to call SNP genotypes and infer haplotypes for a single individual given reads produced by whole-genome shotgun sequencing using high-throughput technologies such as 454, Illumina, and ABI SOLiD.  GeneSeq yields high genotype calling accuracy even from low read coverage by ecploting linkage disequilibrium patterns extracted from a reference panel such as those generated by the international Hapmap project.  Genotype and haplotype inference is  performed efficiently using a hierarchical factorial hidden Markov model (HF-HMM) integrating allele coverage information extracted from read data with haplotype frequencies inferred from the reference panel.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GeneSeq

:: MORE INFORMATION

J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu,
Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads,
BMC Bioinformatics 12(Suppl 1):S53, 2011

GEDI-ADMX 1.03 – GEDI for Admixed Populations

GEDI-ADMX 1.03

:: DESCRIPTION

GEDI-ADMX package provides methods for

local ancestry inference
SNP genotype error detection and correction
imputation of missing genotypes at typed SNPs, and
imputation of genotypes at untyped SNPs
in admixed populations based on whole-genome SNP genotype data and reference haplotype panels for ancestral populations.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

GEDI-ADMX for linux ; for windows

:: MORE INFORMATION

Citation:

J. Kennedy and I.I. Mandoiu and B. Pasaniuc,
Genotype Error Detection using Hidden Markov Models of Haplotype Diversity,
Journal of Computational Biology 15, pp. 1155-1171, 2008,

GEDI 1.03 – Genotype Error Detection & Imputation

GEDI 1.03

:: DESCRIPTION

GEDI package provides methods for

* error detection in whole-genome SNP genotype data
* recovery of missing SNP genotypes
* imputation of genotypes at untyped SNPs based on reference haplotypes such as those provided by the Hapmap project
* genotype phasing through a copy of our highly scalable ENT algorithm.

GEDI handles genotype data from unrelated individuals as well as individuals related by simple pedigrees such as trios. GEDI computations rely on efficient likelihood computations based on a Hidden Markov Model of haplotype diversity in the population under study.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GEDI

:: MORE INFORMATION

Citation:

J. Kennedy and I.I. Mandoiu and B. Pasaniuc,
Genotype Error Detection using Hidden Markov Models of Haplotype Diversity,
Journal of Computational Biology 15, pp. 1155-1171, 2008,