Sniper 1.6.4 – SNP Discovery Utilizing Multi-mapping Reads

Sniper 1.6.4

:: DESCRIPTION

Sniper is a Bayesian probabilistic model that enables SNP discovery in both unique and repetitive regions of a genome by utilizing the information from multiply-mapped sequence reads.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux/ MacOsX/ Windows
  • Python

:: DOWNLOAD

 Sniper

:: MORE INFORMATION

Citation

Genome Biol. 2011 Jun 20;12(6):R55. doi: 10.1186/gb-2011-12-6-r55.
Sniper: improved SNP discovery by multiply mapping deep sequenced reads.
Simola DF, Kim J.

hapassoc 1.2-8 – Inference of Trait Associations with SNP Haplotypes and other attributes using the EM Algorithm

hapassoc 1.2-8

:: DESCRIPTION

The hapassoc R package implementing methods described in Burkett et al. (2004) for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 hapassoc

:: MORE INFORMATION

Citation

Burkett et al. (2004)
A note on inference of trait associations with SNP haplotypes and other attributes in generalized linear models.
Hum Hered. 2004;57(4):200-6.

LDheatmap 1.0-4 – Graphical Display of Pairwise Linkage Disequilibria between SNPs

LDheatmap 1.0-4

:: DESCRIPTION

LDheatmap is an R package implementing a graphical tool for exploring pairwise linkage disequilibria between Single Nucleotide Polymorphisms (SNPs).

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 LDheatmap

:: MORE INFORMATION

Citation

Ji-Hyung Shin, Sigal Blay, Brad McNeney, Jinko Graham
LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms
Journal of Statistical Software Vol. 16, Code Snippet 3, Sep 2006

MACLEAPS 1.0.2 – Machine Learning Analysis Pipeline for Genome-Wide Accociation Study SNP data

MACLEAPS 1.0.2

:: DESCRIPTION

MACLEAPS is an automated pipeline that uses state-of-the-art machine learning algorithms to create a disease risk model based on a given GWAS SNP dataset and assesses its predictive performance for unseen datasets. The pipeline can either use a first dataset for training the model and a second for validation, or perform a nested k-fold cross-validation on a single dataset.

::DEVELOPER

the Interfaculty Institute for Biomedical Informatics (IBMI) (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • PLINK
  • Java

:: DOWNLOAD

  MACLEAPS

:: MORE INFORMATION

Citation

Hum Mutat. 2012 Dec;33(12):1708-18. doi: 10.1002/humu.22161. Epub 2012 Aug 3.
Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities.
Mittag F et al.

SNPPar V1.0 – Parallel/Homoplasic SNP Finder

SNPPar V1.0

:: DESCRIPTION

SNPPar is designed to find homoplasic SNPs based on a user-defined phylogenetic tree

::DEVELOPER

SNPPar team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SNPPar

:: MORE INFORMATION

Citation

Edwards DJ, Duchene S, Pope B, Holt KE.
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
Microb Genom. 2021 Dec;7(12). doi: 10.1099/mgen.0.000694. PMID: 34874243.

Admixture 1.3.0 – Fast Ancestry Estimation

Admixture 1.3.0

:: DESCRIPTION

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

::DEVELOPER

David Alexander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

Admixture

:: MORE INFORMATION

Citation

Fast model-based estimation of ancestry in unrelated individuals.
Alexander DH, Novembre J, Lange K.
Genome Res. 2009 Sep;19(9):1655-64. doi: 10.1101/gr.094052.109.

BMC Bioinformatics. 2011 Jun 18;12:246. doi: 10.1186/1471-2105-12-246.
Enhancements to the ADMIXTURE algorithm for individual ancestry estimation.
Alexander DH, Lange K.

ChroMoS – SNP Classification, Prioritization and Functional Interpretation

ChroMoS

:: DESCRIPTION

ChroMoS (Chromatin Modified SNPs) combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.

::DEVELOPER

Bioinformatics and Next Generation Sequencing Group; Max Planck Institute of Immunobiology and Epigenetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation.
Barenboim M, Manke T.
Bioinformatics. 2013 Sep 1;29(17):2197-8. doi: 10.1093/bioinformatics/btt356.

SNP-VISTA 1.0 – SNP Visualization tool

SNP-VISTA 1.0

:: DESCRIPTION

SNP-VISTA is an interactive SNP visualization tool.

GeneSNP-VISTA: Visualization of mutations in genes

EcoSNP-VISTA – Visualization of SNPs and discovery of recombination points in microbial populations

::DEVELOPER

Inna Dubchak at U.S. Department of Energy Joint Genome Institute

:: SCREENSHOTS

SNP-VISTA

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

 GeneSNP-VISTA , EcoSNP-VISTA

:: MORE INFORMATION

Citation

Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak I
SNP-VISTA: An interactive SNP visualization tool,
BMC Bioinformatics 2005, 6:292

snp.plotter 0.5.1 – SNP/haplotype Association and Linkage Disequilibrium plotting package

snp.plotter 0.5.1

:: DESCRIPTION

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values.

::DEVELOPER

Augustin Luna, Kristin Nicodemus (email: augustin@mail.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snp.plotter

:: MORE INFORMATION

Citation

Luna, Nicodemus (2007),
snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package“,
Bioinformatics, 23(6):774-776.

SNPEVG 3.2 – SNP Effect Viewing and Graphing

SNPEVG 3.2

:: DESCRIPTION

SNPEVG is a graphical tool for SNP effect viewing and graphing.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ MacOsX

:: DOWNLOAD

 SNPEVG

:: MORE INFORMATION

Citation

Wang, S., D. Dvorkin, and Y. Da.
SNPEVG: a graphical tool for GWAS graphing with mouse clicks.
BMC Bioinformatics.2012, 13:319.