simtrait – Simulate Complex Traits from Genotypes

simtrait

:: DESCRIPTION

The simtrait R package enables simulation of complex traits with user-set number of causal loci and the desired heritability of the trait (the proportion of variance due to genetic effects).

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

simtrait

:: MORE INFORMATION

Genonets 201805 – Analysis and Visualization of Genotype Networks

Genonets 201805

:: DESCRIPTION

Genonets Server is a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations that facilitate exploratory research and education.

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genonets server-a web server for the construction, analysis and visualization of genotype networks.
Khalid F, Aguilar-Rodríguez J, Wagner A, Payne JL.
Nucleic Acids Res. 2016 Apr 22. pii: gkw313.

SimPed – Generate Haplotype and Genotype data for Pedigree Structures

SimPed

:: DESCRIPTION

SimPed is a program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies.

::DEVELOPER

Human Genome Sequencing Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows  / Linux / MacOsX

:: DOWNLOAD

 SimPed

:: MORE INFORMATION

Citation

Leal, Yan, Muller-Myhsok (2005),
SimPed: a simulation program to generate haplotype and genotype data for pedigree structures“,
Human Heredity, 60(2):119-122.

MimicrEE – Simulating Genotypes and Phenotypes in experimentally evolving populations

MimicrEE

:: DESCRIPTION

MimicrEE (Mimicing Experimental Evolution) is a tool for forward simulations of entire genomes. It basically allowes to simulate adaptation from standing genetic variation, thus no ‘de novo’ mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

MimicrEE

:: MORE INFORMATION

GQT 1.0 – Genotype Query Tools

GQT 1.0

:: DESCRIPTION

GQT is command line software and a C API for indexing and querying large-scale genotype data sets like those produced by 1000 Genomes, the UK100K, and forthcoming datasets involving millions of genomes.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GQT

:: MORE INFORMATION

Citation:

Nat Methods. 2016 Jan;13(1):63-5. doi: 10.1038/nmeth.3654. Epub 2015 Nov 9.
Efficient genotype compression and analysis of large genetic-variation data sets.
Layer RM, Kindlon N, Karczewski KJ; Exome Aggregation Consortium, Quinlan AR

minimac 2 2014.9.15 – Faster Genotype Imputation

minimac 2 2014.9.15

:: DESCRIPTION

minimac is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 minimac2

:: MORE INFORMATION

Citation:

minimac2: faster genotype imputation.
Fuchsberger C, Abecasis GR, Hinds DA.
Bioinformatics. 2014 Oct 22. pii: btu704.

Gigwa 2.2 – Genotype Investigator for Genome Wide Analyse

Gigwa 2.2

:: DESCRIPTION

The Gigwa application provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time.

:: DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

Gigwa

:: MORE INFORMATION

Citation

Gigwa v2-Extended and improved genotype investigator.
Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P.
Gigascience. 2019 May 1;8(5). pii: giz051. doi: 10.1093/gigascience/giz051.

Gigwa-Genotype investigator for genome-wide analyses.
Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P.
Gigascience. 2016 Jun 6;5:25. doi: 10.1186/s13742-016-0131-8.

PlasmidTron 0.4.1 – Assembling the cause of Phenotypes and Genotypes from NGS data

PlasmidTron 0.4.1

:: DESCRIPTION

PlasmidTron utilizes the phenotypic data normally available in bacterial population studies, such as antibiograms, virulence factors, or geographical information, to identify traits that are likely to be present on DNA that can randomly reassort across defined bacterial populations. It is also possible to use this methodology to associate unknown genes/sequences (e.g. plasmid backbones) with a specific molecular signature or marker (e.g. resistance gene presence or absence) using PlasmidTron. PlasmidTron uses a k-mer-based approach to identify reads associated with a phylogenetically unlinked phenotype.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PlasmidTron

:: MORE INFORMATION

Citation

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data,
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J. Klemm, Nicholas R. Thomson, Jacqueline A. Keane, 2018,
Microbial Genomics 4(3); doi: 10.1099/mgen.0.000164

fastStructure 1.0 – Inferring Population Structure from SNP Genotype data

fastStructure 1.0

:: DESCRIPTION

fastStructure is an algorithm for inferring population structure from large SNP genotype data.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • Numpy
  • Scipy
  • Cython
  • GNU Scientific Library

:: DOWNLOAD

 fastStructure

:: MORE INFORMATION

Citation

fastSTRUCTURE: variational inference of population structure in large SNP data sets.
Raj A, Stephens M, Pritchard JK.
Genetics. 2014 Jun;197(2):573-89. doi: 10.1534/genetics.114.164350

sampletrees 20151127 / Rsampletrees 1.0.2 – Sampling Gene Genealogies Conditional on SNP Genotype data

sampletrees 20151127 / Rsampletrees 1.0.2

:: DESCRIPTION

The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

::DEVELOPER

SFU Statistical Genetics working group

:: REQUIREMENTS

:: DOWNLOAD

 sampletrees / Rsampletrees 

:: MORE INFORMATION

Citation

sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.