PICA – Genotype-phenotype data Mining software

PICA

:: DESCRIPTION

PICA (Phenotype Investigation with Classification Algorithms) is a Python framework for testing genotype-phenotype association algorithms.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PICA

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1834-40. Epub 2010 Jun 6.
Efficient learning of microbial genotype-phenotype association rules.
MacDonald NJ, Beiko RG.

SigniSite 2.1 – Residue level Genotype Phenotype Correlation in Protein Multiple Sequence Alignments

SigniSite 2.1

:: DESCRIPTION

SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Jessen LE1, Hoof I, Lund O, Nielsen M.

GTRAC V0.1.4 – Genotype Random Access Compressor

GTRAC V0.1.4

:: DESCRIPTION

GTRAC is a new algorithm that achieves significant compression ratios while allowing fast random access over the compressed database.

::DEVELOPER

Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

GTRAC

:: MORE INFORMATION

Citation

GTRAC: fast retrieval from compressed collections of genomic variants.
Tatwawadi K, et al.
Bioinformatics 2016. PMID 27587665 Free PMC article.

Geno2pheno 3.4 – Estimating Phenotypic Drug Resistance from HIV-1 Genotypes

Geno2pheno 3.4

:: DESCRIPTION

Geno2pheno is a web server for the prediction of HIV phenotypic drug resistance and coreceptor usage from genotype.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.
Beerenwinkel N, Däumer M, Oette M, Korn K, Hoffmann D, Kaiser R, Lengauer T, Selbig J, Walter H.
Nucleic Acids Res. 2003 Jul 1;31(13):3850-5.

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.