3DSNP

• Description : A database linking noncoding SNPs to 3D interacting genes.

4P

• Description : Computes population genetics statistics from large single nucleotide polymorphism (SNP) datasets. It also includes computation of the joint frequency spectrum.

4Pipe4

• Description : A pipeline tool for analysis and detection of single nucleotide polymorphism (SNP) in 454 EST sequencing data.

AASsites

• Description : A web-based pipeline for analysis of single nucleotide polymorphism (SNP) containing sequences to detect causes for altered splicing pattern.

AbCD

• Description : A web tool that provides pre-estimated effective sample sizes, specific to each minor allele frequency (MAF) category, for designs with arbitrary coverage (0.5-30X) and sample size (20-20,000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans).

AD-LIBS

• Description : A local ancestry inference tool for low-coverage resequencing data.

adegenet

• Description : An R package for analysis of large, genome-wide SNP data.

ADMIXPIPE

• Description : ADMIXPIPE is a pipeline tool for integration of ADMIXTURE analysis with variant call format (VCF) filtering tools to generate file types that can be analyzed by CLUMPAK . Dependencies: PLINK 1.9 beta 4.5 or newer, VCFtools, Admixture

ADMIXTURE

• Description : A tool to estimate individual ancestry from single nucleotide polymorphism (SNP) data sets.

AffyMAPSDetector

• Description : A tool for annotation and characterization of SNP contributions to anomalous probe binding behavior.

AffyPipe

• Description : A software tool combining all Affymetrix software. It also allows editing of SNP probe classes directly and to export genotypes in PLINK format.

ALICE

• Description : an integrated analysis of allele frequency, allelic imbalance, loss of heterozygosity, long contiguous stretch of homozygosity, and copy number variation or alteration based on SNP probe hybridization intensities and genotypes.

ALOHOMORA

• Description : Facilitates genome-wide linkage studies done with high-density single nucleotide polymorphism (SNP) marker panels, such as the Affymetrix GeneChip(R) Human Mapping 10K Array.

Altools

• Description : Uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm for genome segmentation to identify copy number variations. Uses insert size information to detect large deletions.

AMF, AgroMarker Finder

• Description : A tool for restriction site associated data (RAD) analysis for identification of polymorphism, SNPs and indels for rice genome.

AncestrySNPminer

• Description : A web tool to retrieve and develop ancestry informative SNP panels. It also includes various population genomics statistical methods.

AnnTools

• Description : A tool annotating single nucleotide substitutions (SNP/SNV), indels, and copy number variations (CNV) in sequencing and microarray data.

argyle

• Description : An R package for analysis of genotyping Illumina array array data.

ArrayFusion

• Description : A tool to annotate CGH results and microarray data from a range of platforms, such as cDNA, expression, exon, SNP, array-CGH and ChIP-on-chip. It converts the data into standard formats that can be visualized in Affymetrix Integrated Genome Browser and GBrowse in the HapMap Project.

ARTS

• Description : A web-based tool for a set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants.

ASSIsT

• Description : An automatic SNP scoring tool for in- and outbreeding species. Customized pipeline for calling and filtering of SNPs from Illumina Infinium arrays. ASSIsT builds on GenomeStudio-derived data and identifies markers that follow a bi-allelic genetic model and show reliable genotype calls, and re-edits SNP calls.

AssociationViewer

• Description : A application to display single nucleotide polymorphism (SNP) in a genome.

Atlas-SNP2

• Description : A SNP discovery method to assess variant allele probability.

atSNP

• Description : atSNP ( Affinity Test for regulatory SNP detection ) is a tool for computation of affinity scores single nucleotide polymorphism (SNP) and a reference. The atSNP algorithm computes p-values based on position weight matrices (PWMs).

atSNP Search

• Description : atSNP Search is a web-based tool and database for analysis of human genome motifs with reference and variant alleles. The atSNP algorithm assesses and tests the variant alteration significance. atSNP also produces graphical representations of the motif matches. Currently, the database contains over 37 billion variant-motif pairs.

AutoSNPa

• Description : A tool to graphically visualize Affymetrix single nucleotide polymorphism (SNP).

BALL-SNP

• Description : A tool to identify candidate non-synonymous single nucleotide polymorphisms (SNPs) in a single protein by visualizing the mutated residues within the wild type structure. Based on the Biochemical Algorithms Library (BALL).

BAM-matcher

• Description : A tool to determine if two separate BAM files contain reads sequenced from the same sample by counting genotype matches at SNPs.

Bayenv

• Description : Software implementing a Bayesian method that uses a set of markers to estimate a pattern of covariance in allele frequencies between different populations. The estimation is used as a null model for testing individual SNPs.

BGT

• Description : A command-line tool to store and query whole-genome genotypes.

Bis-SNP

• Description : A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and DNA methylation calling in bisulfite treated massively parallel sequencing. Uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine contextto determine genotypes and methylation levels simultaneously.

BSviewer

• Description : A tool to visualize methylation statuses at nucleotide level while preserving the essential information of the sequencing data.

C++ library compression algorithm

• Description : A C++ library algorithm with a file format to compress and retrieve large-scale SNP data useful for large-scale association studies.

CandiSNPer

• Description : A webtool helps to characterize Single Nucleotide Polymorphisms (SNPs) that are located in the maximal Linkage Disequilibrium (LD) region of an SNP of interest.

CASMAP

• Description : Detects statistically significant combinations of single nucleotide polymorphisms (SNPs) in association mapping, and can make corrections of categorical covariates, such as age and gender. The tool is also avalable as an R package.

CerealsDB

• Description : A website for wheat genome provides a range of information, such as SNP markers.

chopsticks

• Description : chopsticks is an R tool containing classes and methods for large-scale single-nucleotide (SNP) association studies.

ChroMoS

• Description : SNP classification, prioritization and prediction of their functional effect. The tool uses a large database of SNPs and chromatin states, and allows a user to upload genetic information.

CircosVCF

• Description : A visualization tool of genome-wide variant data described in VCF files using circos plots. Gives a broad overview of the genomic relationship between genomes, and can focuse on specific SNP regions.

CloVR-Comparative

• Description : A desktop virtual machine providing several automated microbial genomics analysis pipelines, such as 16S, whole genome and metagenome sequence analyses. It also supports use of remote cloud computing resources.

Clumpak

• Description : Clumpak (Clustering Markov Packager Across K) is a tool to automate the postprocessing of model-based population structure analyses. The pipeline includes a pipeline for the summation and graphical representation of the results from a STRUCTURE-like program.

COKGEN

• Description : An R package for Identification of Rare Copy Number Variation from SNP Array Data.

CollapsABEL

• Description : The R package has an implementation of a generalized version of CDH test to detect compound heterozygosity (CH).

ConsensusCluster

• Description : A tool to cluster consensus sequences using PCA for selection if features, aimed for the analysis of high-dimensional single nucleotide polymorphism (SNP) and gene expression microarray data.

Coval

• Description : Short read alignment with filtering and error correction of mismatched reads for accurate identification of DNA polymorphism.

CPAP

• Description : A Cancer Panel Analysis Pipeline (CPAP) uses input files from variant calling software to generate a distribution map of SNPs among all of the samples. It also integrates additional information about the identified SNPs by linking to an integrated SQL database compiled from SNP-related databases, including dbSNP, 1000 Genomes Project, COSMIC, and dbNSFP.

Crossbow

• Description : A pipeline for whole genome re-sequencing. It combines BOWTIE, SoapSNP, and a genotyper.

CSI Phylogeny

• Description : Single nucleotide polymorphism detection and construction of a phylogenetic tree.

CsSNP

• Description : Dection of comparative SNP segments and display detailed information of them.

Database of single nucleotide polymorphism (dbSNP)

• Description : A web-based database for single nucleotide polymorphism (SNP) search.

DBM

• Description : A dynamic Bayesian Markov model (DBM) for simultaneous genotype calling and haplotype phasing in low-coverage NGS data of unrelated individuals.

dbSNP-Q

• Description : A web-based database for information on single nucleotide polymorphism (SNP) in several different organisms.

DECA

• Description : A tool to call copy-number variation (CNV) with ADAM and Apache Spark. The DECA algorithm implements XHMM, including new optimizations, to speed up the computation. It also uses the Viterbi algorithm in logs space and scaled versions of the forward and backward algorithms. Requires: Maven, Spark 2.1.0+, Hadoop 2.7, Scala 2.11.

DHOEM

• Description : DHOEM (densification of haplotypes by loess regression and maximum likelihood) simulates new markers in real SNP marker data and generates a new population.

DiscoSnp

• Description : Software tools to detect single nucleotide polymorphism (SNP) and insertions and deletions (indels) without the need of a reference sequence.
  Additional names: DiscoSnp++, DiscoSnpRad.

DiSNPindel

• Description : Detection of intra-individual SNPs and InDels in direct amplicon sequencing of a diploid. No reference sequence required.

DivStat

• Description : A tool for single nucleotide polymorphism (SNP) analysis of genomic diversity.

DNannotator

• Description : A web tool to de novo annotation of SNPs, STSs, and exons.

DnaSP

• Description : A software package for the analysis of DNA polymorphisms using data from a multiple sequence aligned data. Features: Estimate various measures of DNA sequence variation within and between populations. Estimate linkage disequilibrium, recombination, gene flow and gene conversion parameters. A number of neutrality tests such as, the Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997), Ramos-Onsins and Rozas (2002), Achaz (2009) tests, and compute confidence intervals by the coalescent. Input data formats: FASTA; MEGA; NBRF/PIR; NEXUS; PHYLIP; HapMap3; VCF; Multi-MSA; Arlequin.

ebwt2snp

• Description : A tool to detect single nucleotide polymorphism (SNP) usinh extended Burrows–Wheeler Transform (eBWT), and makes a reference-free evaluation of its accuracy by calculating the coverage of each SNP.

ECOGEMS

• Description : ECOGEMS is a tool to compress into sparse matrices and retrieve SNP data for rice. ECOGEMS has a graphical interface for visualization and downloading SNP data.

ENGINES

• Description : A framework to summarize data from any population based single nucleotide (SNP) genotype database, such as allele frequencies, heterozygosity, F_st, and I_n. The home page has a clickable map to select populations around the world.

Ensemble Variant Effect Predictor (SNP Effect Predictor)

• Description : A web and command-line tool to analyze and predict functional consequences of your variants, SNPs, indels, CNVs on genes, regulatory regions, transcripts, and protein sequences.

Equalizer

• Description : A tool to reduces singlenucleotide polymorphism (SNP) bias in Affymetrix microarrays for accurate assessment of germline influence on gene expression.

EuroForMix

• Description : Evaluation of SNP genotype data in mixed DNA panels.

Evoker

• Description : A tool to visualize genotype cluster plots and provides a storage.

F-SNP

• Description : A Functional Single Nucleotide Polymorphism (SNP) database.

Fast-GBS

• Description : A pipeline to extract a high-quality SNP catalog. INPUT; FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries.

FastSNP

• Description : A web-based tool for the identification of tumor-associated single nucleotide polymorphism (SNP).

fcGENE

• Description : Transforms SNP and imputation results datasets into a variety of formats. Supports SNP data management, quality control, and analysis workflows. Formats - PLINK MACH, IMPUTE, BEAGLE, BIMBBAM, HAPLOVIEW, EIGENSOFT, and SNPTEST.

FEATnotator

• Description : A tool for annotation of sequence features and variation.

Ferret

• Description : A tool to extract human genetic variation data from the latest release of the 1000 Genomes (1KG) Project. I can compute allelic frequencies for 1KG populations and for the Exome Sequencing Project populations. Data can be imported into popular pre-existing tools, e.g., PLINK and HaploView.

FitTetra and fitPoly

• Description : A genotype calling tools for tetraploid and polyploid species with multiple population and parental data support.

Flapjack

• Description : A tool for analysis and visualization of large volumes of single nucleotide polymorphism (SNP). The realtime graphical rendering allows comparison between lines, markers, and chromosomes.

flashpca

• Description : A tool for principal component analysis (PCA) of single nucleotide polymorphism (SNP) data.

FROG-kb

• Description : A Web tool for forensic practice. FROG-kb focuses on single nucleotide polymorphisms (SNPs) and has reference population data for various published panels of individual identification SNPs (IISNPs), and many published panels of ancestry inference SNPs (AISNPs). FROG-kb calculates random match probabilities (RMP) and relative likelihoods of ancestry for a genotype profile provided by a user.

FunciSNP

• Description : A tool to integrate functional non-coding data sets with genetic association studies for identification of regulatory SNPs.

FunctSNP

• Description : An R package to link single nucleotide polymorphism (SNP) to function knowledge. dbAutoMaker generates a local database.

G-SNPM

• Description : A GPU (Graphics Processing Unit) based tool to map SNPs on a genome against a reference sequence.

GACT

• Description : Genome Build and Allele Definition Conversion Tool. It predicts and converts between any of the common SNP allele definitions and between the major genome builds.

GARLIC

• Description : A model-based method for inferring ROH in genome-wide SNP datasets with population-specific parameters and a genotyping error rate. A classification module to identify biologically interesting classes of ROH.

GARLIC Viewer

• Description : Connects human diseases/traits with cell types/tissues based on overlaps between disease-associated genetic variants and cis-regulatory elements. It can be used to retrieve potential disease-causative genetic variants overlapping specific regulatory sequences.

GCTA

• Description : Genome-wide complex trait analysis. GCTA estimates the variance explained by all the SNPs on a sequence for a complex trait, instead of testing associations of each individual SNP.

GeDi

• Description : GeDi is a tool to call single nucleotide variants (SNV). The GeDi algorithm uses suffix-arrays and can define SNVs at complex variant loci and at low allele frequencies.

GeneCards

• Description : A comprehensive web resource for human genes and diseases.

GeneEvolve

• Description :  A tool for forward-time simulator of realistic whole-genome sequence and SNP data.

GeneMarker HTS

• Description : A workflow for forensic and medical research mitochondrial DNA data analysis from massively parallel sequencing (MPS) systems. Generates an exportable consensus mtDNA sequence that produces phylogenetically correct SNP and INDEL calls using a customizable motif-based alignment algorithm.

GeneNetwork

• Description : Workflows and methods, collections of genetic, genomic, and phenotype data for large families. Statistical analysis and gene mapping software for analysis of regulatory networks and genotype-to-phenotype relations. Graphical displays of variation in gene expression or other phenotypes, scatter plots of pairs of traits (Pearson or rank order), construction of both simple and complex network graphs, analysis of principal components and synthetic traits, QTL mapping using marker regression, interval mapping, and pair scans for epistatic interactions.

genepopedit

• Description : Tool for manipulating multilocus molecular data in R.

GenoExp

• Description : A web tool for prediction of gene expression levels from single nucleotide polymorphisms (SNPs).

Genomic Oligoarray and SNP array evaluation tool

• Description : A tool for educational purposes for health care providers.

GenomicTools (The R-package GenomicTools)

• Description : A collection of tools for the analysis of expression and genotype data, such as Multifactor Dimensionality Reduction (MDR) for the identification of SNP-SNP interactions.

Genotype harmonizer

• Description : A tool for file format conversion for pooled data. It solves unknown strands by aligment of A,T and G,C single nucleotide polymorphisms (SNPs) to a reference sequence, using linkage disequilibrium patterns. Supported file formats: PLINK, binary PLINK, VCF, SHAPEIT2, and Oxford GEN.

GenotypeColour

• Description : A tool for colour visualisation of SNPs and CNVs.

GenPlay

• Description : A multipurpose graphical genome analyzer. It displays tracks for gene structure, gene expression, repeat families, CPG islands, and custom tracks, e.g., RNA-Seq, Chip-Seq, TimEX-Seq, and single nucleotide polymorphism (SNP). It can also generate statttistics for minimum, maximum, SD, and correllation. The tool has Gaussian filter, peak finders, signal saturation, island finders, scatter plots, and bar charts.

GenPlay Multi-Genome

• Description : A comparison of allele-specific expression and functional genomic data. It allows an analysis of custom genome data and to analyze variants to compare genome assemblies.

Gigwa-Genotype

• Description : A web site containing a wide range of databases and analysis tools. Allows the data to be exported in many different formats.

GLANET

• Description : A sequence annotation and enrichment analysis tool for GC content, assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis.

GMFilter and SXTestPlate

• Description : Tools for SNPlex genotypingsystem.

gmRAD

• Description : a tool for calling SNP genotypes across a hybrid population with RAD-seq data for genetic linkage mapping.

GRACOMICS

• Description : A tool to compare results from various large-scale omics analysis methods. It can produce correlations plots, multiple results heat maps, and interactive summary plot from two separate results.

GW-SEM

• Description : Genome-Wide Structural Equation Modeling. A method to test the association of a SNP with multiple phenotypes or a latent construct on a genome-wide basis using a diagonally weighted least squares (DWLS) estimator for four common SEMs; a one-factor model, a one-factor residuals model, a two-factor model, and a latent growth model.

Haplo2Ped

• Description :

HaploPainter

• Description : Draws pedigrees with complex haplotypes, obtained by using for genome scans of marker panels of single nucleotide polymorphisms (SNPs).

HapZipper

• Description : A compression tool to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma.

Heap

• Description : SNP calling in low coverage NGS data, aligned to the reference genome sequences. Heap determines genotypes and calls SNPs.

HGVbase

• Description : A web portal summarizing all known sequence variations in the human genome.

HLA-check

• Description : Detects aberrant HLA allele calling in respect to SNP genotypes. Increases HLA imputation software accuracy.

HMDB

• Description : A database dontaining information about small molecule metabolites in human. Tools for text, sequence, chemcal structure searches.

HUMA

• Description : The Human Mutation Analysis (HUMA) database and web server. analysis of genetic variation in humans. HUMA integrates sequence, structure, variation, and disease data into a single, connected database. Users can upload their private variation datasets, which are automatically mapped to public data and can be analyzed. The interface provides data access and visualization, and RESTful Web API provides programmatic access to the data.

HYSYS

• Description : Methods to measure sample relatedness and identify potential swaps and contamination.

IBDfinder and SNPsetter

• Description : Tools to display graphical plots identifying runs of homozygous single nucleotide polymorphisms (SNPs) in Affymetrix SNP chip data.

iCTNet

• Description : A Cytoscape plugin to analyze complex traits networks.

IDCheck

• Description : A tool for comparison of the identity of RNA-seq reads and SNP genotypes using a likelihood based method.

IMHOTEP

• Description : A webserver. Computes a composite score by integration of several tools for predicting functional consequences of non-synonymous SNPs.

InSNP

• Description : A tool for SNP and indel detection.

inTB

• Description : A web-based application for analysis of clinical and molecular data of tuberculosis.

Introgression browser (iBrowser)

• Description : Visualizes introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) and filters out heterozygous SNPs, multi-nucleotide polymorphisms and insertion-deletions.

IntSIM

• Description : Simulates common DNA variants and generates sequencing reads for mixture genomes. Features; 1. Simulates both germline and somatic variants, 2. Generates reads corresponding to heterogeneous genomes and produces tumor-normal matched samples, 3. Simulates correlations among SNPs, among CNVs/CNAs based on HMM models, 4. Simulates broad and focal CNV/CNA events.

ISMU

• Description : A pipeline integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays.

ITALICS

• Description : A tool to normalize Affymetrix GeneChip Human Mapping 100K and 500K sets.

JEPEG

• Description : Imputes summary statistics at unmeasured eQTLs and tests for the joint effect of measured and imputed eQTLs affecting a gene function/expression on a phenotype.

JEPEGMIX

• Description : Direct Imputation of summary Statistics of unmeasured SNPs from

JEPEGMIX2

• Description : A tool for gene-level Joint Analysis of functional SNPs in Cosmopolitan Cohorts by using heterogeneous panels.

KASPspoon

• Description : A tool for high-throughput single nucleotide polymorphism (SNP) genotyping. It simulates a PCR and then compares in vitro and in silico PCR results. The tool reports amplimers close to or adjoining genes, SNPs, simple sequence repeats, and those that are shared between in vitro and in silico PCR results for selection of the most appropriate amplimers. It also compares physical and genetic maps to report the primer set genome coverage for PCR-walking.

KinSNP

• Description : Homozygosity mapping using SNP arrays. The software searches for a range of SNPs that are homozygous in ascertained sick individuals.

kSNP

• Description : Finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation. kSNP3 now available.

KvarQ

• Description : Performs in silico genotyping for selected loci, e.g., single nucleotid polymorphism and drug resistance.

LAMPLINK

• Description : Detects statistically significant SNP combinations from genome-wide case-control data.

LAVA

• Description : NGS-based genotyping algorithm for a set of SNP loci. Takes advantage of matching of mid-size k-mers (with k 

LDlink

• Description : A suite of web applications to assess haplotype structures and linkage of funtional variants.

Lep-MAP

• Description : Lepidoptera-MAP (Lep-MAP, Lep-MAP2, Lep-MAP3), is tool for constructing linkage maps with ultradense genome-wide SNP data.

Lep-MAP3

• Description : Linkage mapping software for mapping high-throughput whole genome sequencing datasets. Allows cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for thousands of individual samples. Can be used for validation and refinement of de novo genome assemblies. It can analyse low-coverage datasets.

LincSNP 2.0

• Description : Database of linking disease-associated SNPs to human large intergenic non-coding RNAs.

linkSNPs

• Description : A tool to detect single nucleotide polymorphism (SNP) and to reconstruct haplotypes of a diploid organism, i.e., it can identify SNPs originating from each parent. The linkSNPs algorithm requires, on average, five heterozygous sites per kilobase of sequence.

LIST

• Description : A web-based tool to predict the effect of amino acid mutations in protein sequences by pair-wise alignments of protein sequences in the UniProt Swiss-Prot/TrEMBL database and estimates deleteriousness utilizing a taxonomic distance of the species.

logicFS

• Description : A tool to identify single nucleotide polymorphism (SNP) interactions. The logicFS algorithm uses logic regression among binary variables to identify SNP interactions that can explain the disease status in case-control studies.

MADAP

• Description : A clustering tool for genome annotation data mapped onto genome sequences, such as counts, probabilitites, intensities, SNP typing.

MapNext

• Description : An automated SNP detection from population sequences for spliced and unspliced alignments of short reads and.

Mapsnp

• Description : The tool uses the biomaRt and the rtracklayer packages to annotate queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. mapsnp package inherits from the Gviz package.

MAVIANT

• Description : Multipurpose Alignment Viewing and Annotation Tool. A tool for viewing polymorphic sites in DNA chromatograms.

METAINTER

• Description : A tool to perform meta-analysis of summary statistics of related studies, such as single-marker association tests.

MethGo

• Description : Analysis of data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS). Analyses- 1. coverage distribution of each cytosine; 2. global cytosine methylation level; 3. cytosine methylation level distribution; 4. cytosine methylation level of genomic elements; 5. chromosome-wide cytosine methylation level distribution; 6. Gene-centric cytosine methylation level; 7. cytosine methylation levels at transcription factor binding sites (TFBSs); 8. single nucleotide polymorphism (SNP) calling; 9. copy number variation (CNV).

Micro-Analyzer

• Description : A tool for the preprocessing of Expression and SNPs Affymetrix microarray.

MicroSNiPer

• Description : Predicts the impact of a SNP on putative microRNA targets.

miRdSNP

• Description : A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes.

MOCSphaser

• Description : MOCSphaser is a tool to infer haplotypes and alleles from copy number variation (CNV) and single nucleotide polymorphism (SNP) data. The MOCSphaser algorithm uses expectation-maximization (EM) and can handle ambiguously determined copies originated from noisy data.

Monovar

• Description : Monovar is a tool for the detection of single-nucleotide variation (SNV). The Monovar analysis algorithm assumes data from separate loci be independent and accounts for sequence coverage variations.

MOODS

• Description : Motif Occurrence Detection Suite for matching position weight matrices (PWMs) against DNA sequences. These tools can handle PWMs containing dependencies among adjacent positions, such as SNPs, insertions, and deletions. It can be as a standalone analysis tool or a component other programs.

MPAgenomics

• Description : An R package for analysis of genomic markers.

mPSQed

• Description : Multiplex PyroSeQuencing EDitor, a software to design of multiplex Pyrosequencing Assays.

mrsFAST-Ultra

• Description : A single nucleotide polymorphism (SNP) aware short read mapper.

mrSNP

• Description : Software to detect SNP effects on microRNA binding.

MSQT

• Description : A comman-line tool to extract single nucleotide polymorphism (SNP) data from multiple sequence alignments, stores it in a database, and provides a web interface to query the database.

MultiBLUP

• Description : A tool for prediction of complex traits using genome-wide single nucleotide polymorphism (SNP).

MultiPSQ

• Description : A tool for pyrosequencing results. Classification of organisms.

MultiRes

• Description : A tool for discriminating rare sequence variants from sequencing errors in Next Generation Sequencing (NGS) data.

mutation3D

• Description : A web application to predict and visualize spatial amino acid structures and substitutions.

MutationTaster

• Description : A web tool for predicting a disease causing potential of single nucleotide polymorphism (SNP) and single amino acid substitutions.

MutDB

• Description : A web-bassed tool to associate Swiss-Prot protein structures with annotated SNPs in dbSNP and amino acid substitutions.

NASP

• Description : A tool to identify Single nucleotide polymorphism in wholle genome sequencing data.

ngs_backbone

• Description : A pipeline (a wrapper) for next-generation (NGS) and Sanger sequence analysis. It can filter reads, map agaist a reference sequence, find single nucleotide polymorphism (SNPs), short sequence repeats (SSRs), and do funtional annotation.

NovelSNPer

• Description : A web tool to classify sequence variants based on the gene structure information in Ensembl.

novoCaller

• Description : a de novo variant calling algorithm that uses information from sequence data in the pedigree and unrelated samples.

NucDiff

• Description : A tool to locate and categorize differences between two closely related nucleotide sequences. The results can be uploaded into genome browser for visualization.

Ohana

• Description : Admixture analysis and population tree estimation for SNP and NGS data.

OpenADAM

• Description :

PANTHER Database and Tools

• Description : Protein classification to ease high-throughput analyses. Classification is by family and subfamily, molecular function, biological process, and pathway. Updated single-nucleotide polymorphisms (SNP) scoring tool.

Patrocles

• Description : A database of polymorphic miRNA-mediated gene regulation in vertebrates.

PBAT

• Description : A tool for family-based association studies. It can accomodate missing parental genotypes, pedigrees with missing genotypes, and analysis of single nucleotide polymorphism (SNPs).

PEAS

• Description : Basic, commonly used single nucleotid polymorphism (SNP) analysis tools.

PHYLOViZ

• Description : Phylogenetic inference and data visualization.

Phyre2

• Description : A web-based suite of tools to predict and analyze protein structure, function and mutations. It has advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants, e.g., non-synonymous SNPs.

pibase

• Description : pibase is a command-line tool to validate single nucleotide polymorphism (SNP) in diploid and haploid genomes, exome data, and in targeted enrichment data. The pibase algorithm works by extracting features at specified coordinates in alignment files and identifies reproducible genotypes.

Pipeliner

• Description : Evaluates the performance of bioinformatics pipelines for next‐generation resequencing.

PolyPhen-2

• Description : From input of non-synonymous single nucleotide polymorphism (SNP), this tool uses analysis of multiple sequence alignments and protein stuctures to predict, annotate, and visualize SNP features. PolyPhen-2 is further development of PolyPhen.

PolySearch

• Description : A web portal for searching associations between human diseases, genes, mutations, drugs and metabolites. See also PolySearch2 V2.

PoolHap

• Description : A tool for inferring haplotype frequencies from pooled samples.

PoPoolation

• Description : A pipeline for analysing pooled next generation sequencing data. It calculates Tajima’s Pi, Watterson’s Theta and Tajima’s D.

PoPoolation DB

• Description : A web tool for analysing pooled next generation sequencing data. It calculates Tajima’s Pi, Watterson’s Theta and Tajima’s D.

PoPoolation2

• Description : A tool to compare allele frequencies for single nucleotide polymorphism (SNP) between two or more populations.

PredictSNP

• Description : Both web-based and comman-line application to predict disease related mutations.

PredictSNP2

• Description : A classifier, combining the output from CADD, FATHMM, DANN, GWAVA, and FunSeq2 to evaluate pathogenic effects in a human genome. The tool provides corresponding annotations from dbSNP, HaploReg, RegulomeDB, GenBank, Clinvar, OMIM, UCSC, and Ensembl databases.

Primer-BLAST

• Description : A tool to design target-specific primers for polymerase chain reaction. Te tool achieves its sensitivity by a combination of BLAST and a global alignment algorithm to get a full primer-target alignment.

PSESM

• Description : A tool for detecting SNP main effects and SNP-SNP interactions.

pulver

• Description : An R package to compute p-values for the interaction term in a very large number of linear regression models.

PupaSNP Finder

• Description : A web-based tool for finding SNPs with putative effect.

PupasView

• Description : A web-based SNP analysis tool for a selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect.

PyHLA

• Description : HLA association analysis: summary, association analysis, zygosity test and interaction test. 

PyroHMMsnp

• Description : A tool for single nucleotide polymorphism (SNP) calling for 454 and Ion Torrent data.

qpure

• Description : An R script that uses copy-number and B allele frequency data from Illumina Omni 1M genotyping (SNP) arrays to assess the tumour content (cellularity) of cancer tissue samples.

QQ-SNV

• Description : A tool to detect single nucleotide polymorphism (SNP) in heterogeneous virus population from Illumina sequencing data. The QQ-SNV algorithm uses a logistic regression classifier model based on quantiles of quality scores.

QR Concordance (QRC)

• Description : Uses a small set of Single nucleotide polymorphisms (SNPs) to uniquely identify a personal genome.

QualitySNPng

• Description : A user-friendly SNP detection and visualization tool. It Uses a haplotype-based strategy to identify reliable SNPs. It is optimized for the analysis of RNA-seq data, but it can also be used on genomic DNA sequences.

QuASAR

• Description : An R package, implementing a statistical method for: i) genotyping from next-generation sequencing reads, and ii) conducting inference on allelic imbalance at heterozygous sites. The sequencing data can be RNA-seq, DNase-seq, ATAC-seq or any other type of high-throughput sequencing data.

QuASAR-MPRA

• Description : A development of allele specific analysis QuASAR (quantitative allele-specific analysis of reads)(https://github.com/piquelab/QuASAR). QuASAR-MPRA analyzes allele specific signals in barcoded read counts data from MPRAs. It accounts for the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors.

QuickSNP

• Description : A web resource for selecting of TagSNPs.

RAiSD

• Description : A parameter free tool to detect selective sweeps using multiple signatures and enumeration of single nucleotide polymorphism (NP) vectors.

RASER

• Description : A short-read aligner for applications for SNPs, RNA editing sites in RNA-Seq data sets.

rehh

• Description : A tool to detect the footprints of recent or ongoing selection of homozygosity.

ReMo-SNPs

• Description : A tool for identification of functional SNPs in regions and motifs genome-wide. Output data ready for a subsequent association study.

RExPrimer

• Description : A web tool for PCR primer design. It increases effectiveness by avoiding 3' SNPs.

RHE_reg

• Description : A method leveraging randomized Method-of-Moments (MoM) estimator of single nucleotide polymorphism (SNP) heritability and genetic correlations in a scalable randomized Method-of-Moments (MoM) estimator for SNP heritability and genetic correlations in linear mixed models (LMMs).

RPPApipe

• Description : Pipeline for the analysis of reverse-phase protein array data.

rSNP_Guide

• Description : Web-based tools for studying SNPs and site-directed mutations in transcription factor binding sites.

RTeQTL

• Description : A Web-based database tool gives eQTL association results. The following tools are included: (1). Single-nucleotide polymorphism (SNP) and (2). Two-SNP conditional eQTL effects on gene expression, 3. A database based on lymphoblastoid cell lines from more than 900 samples with genotypes for two million SNPs in the Hapmap Project used for imputation. The datasets are available from Affymetrix and Immlumina platforms.

SAQC

• Description : A tool for visualization and evaluation of genome-wide SPN array data.

SBVB

• Description : Simulates complex traits using real sequence data and outputs new offspring genomes and phenotypes.

SCcaller

• Description : A tool for detection of single nucleotide polymorphism (SNP) and short insertions and deletions (indels) in data from single-cell sequencing.

SD Plots - Synergy Disequilibrium Plots

• Description : A visualisation tool for genome-wide association data, disease-associated haplotypes, epistatically interacting loci, and provides visual signatures of multivariate correlations of genetic markers.

Seq-SNPing

• Description : SNP discovery, ID identification, editing, and visualizating of sequence alignments.

SeqDoC

• Description : A Perl script to detect mutations by a comparison of DNA sequence chromatograms.

SHOREmap v3.0

• Description : R package, an extention of the short read analysis pipeline SHORE for genotyping.

SIFT

• Description : A web tool to predict the effect of single nucleotide polymorphism (SNP) on protein function.

SInC

• Description : Simulates single nucleotide polymorphism (SNP), insertions and deletions (indels), and copy number variation (CNV).

SMuRF

• Description : An R package for selection of regulatory elements, single nucleotide variants (SNVs), single nucleotide polymorphisms (SNPs), and is-regulatory elements (CREs) using random forests.

SNAP

• Description : A gene prediction tool loosely based on HMM. It has functionality to generate graphical plots.

Snap2

• Description : Predicts effects of single amino acid substitutions (SNPs), using neural networks. Visualizes prediction scores as a heatmap.

SNeP

• Description : Estimates trends in effective population size trajectories using genome-wide SNP data. A user can adjust parameters for sample size, mutation, phasing, and recombination rate.

SNIP-Seq

• Description : A tool to detect single nucleotide polymorphism (SNP) in Illumina sequence data from population samples. The SNIP-Seq algorithm uses quality values of the sequenced bases and iterative estimates of genotypes and error rates based on multiple individuals.

SNiPlay

• Description : Web-based tool, polymorphism discovery and analysis. 1. A pipeline combining tools to detect SNPs and to compute statistical indices and graphical layouts for SNP data. It sends sequences and genotyping data into a series of modules; physical mapping to a reference genome, annotation, SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). 2. A database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects.

SNiPlay3

• Description : A web tool for pipelines to detect, manage, and analyze SNPs and indels.

SNiPloid

• Description : A tool to discover and validate predicted single nucleotide polymorphisms (SNPs), optimized for allopolyploid species.

SNIT

• Description : A pipeline to identify microbial strains.

SNP Cutter

• Description : Designs PCR-RFLP assays on a batch of SNPs from the human genome. Can design primers for natural PCR-RFLP and mismatch PCR-RFLP.

SNP-RFLPing

• Description : Mining of restriction enzyme sites. Provides PCR-RFLP information with multiple functionality about SNPs; SNP retrieval to multiple species, polymorphism types - bi-allelic, tri-allelic, tetra-allelic or indels. Gene-centric searching, HapMap tagSNPs, and gene ontology-based searching - miRNAs, and SNP500Cancer.

snp-search

• Description : A management of single nucleotide polymorphisms (SNPs). It creates a local SQLite database and schema and outputs requested objects. The output contains detailed information about each SNP that can be filtered in various ways.

SNP-sites

• Description : Rapid efficient extraction of SNPs from multi-FASTA alignments.

SNP-VISTA

• Description : SNP-VISTA consists of two versions: GeneSNPVISTA for mapping single nucleotide polymorphism (SNP) and EcoSNP-VISTA detects homologous recombination points in microbial populations.

SNP2RFLP

• Description : A web-based too to identify region-specific SNPs from the NCBI mouse SNP database, being informative between the mouse strains used in a cross. It identifies SNPs that create restriction fragment length polymorphisms (RFLPs) that can be easily assayed.

SNP@Domain

• Description : A web-based tool for identification of single nucleotide polymorphism (SNP) in human protein domains.

SNPAnalyzer 2.0

• Description :

SNPbox

• Description : A web-based primer design tool with modules for single mucleotide polymorphism (SNP)

SNPchiMp v.3

• Description : A web-based tool that allows researchers to browse between various SNP chips and types of information in many species, such as list SNPs that are contained in commercial SNP chips, chromosome and physical position of your SNPs, make commercial SNP/probe names linked to a [rs/ss]IDs, access to sender original information, including orientation, strand, etc., access to Illumina’s FORWARD/REVERSE or TOP/BOT allele coding customized to the desired SNP chip(s), Obtain the latest version of the Interbull SNP exchange index, interact with Ensembl BioMart and Variant Effect Predictor (VeP) tools directly, and Access the open-source (or open-access for third parties) tools for basic SNP data management.

SNPchip

• Description : An R package to plot single nucleotide polymorphism (SNP) data.

SNPConvert

• Description : A set of programs to convert single nucleotide polymorphism (SNP) array, allele coding, and genomic coordinate formats.

Snpdat

• Description : Single nucleotide polymorphisms (SNP) annotation tool. It also provides analyses for non-model organisms.

SNPdetector

• Description : Automated identification of SNPs and mutations in fluorescence-based resequencing reads (Sanger sequencing reads).

SNPduo

• Description : A tool for analysis and visualization of Single Nucleotide Polymorphism (SNP) relatedness between two individuals. The SNPduo algorithm uses identity by a state to identify relatedness. The web implementation generates UCSC UCSC Genome Browser viewable tracks SNPduo.

SNPeffect

• Description : A database for phenotyping human single nucleotide polymorphisms (SNPs).

snpEnrichR

• Description : An R package for analysis of co-localization of single nucleotide polymorphism (SNP).

SNPest

• Description : A tool to generate probabilistic graphical models for estimating genotypes.

SNPexp

• Description : A web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest (eQTL)

SNPFile

• Description : A library for manipulating large SNP datasets with associated meta-data.

SNPGenie

• Description : A command-line tool to estimate evolutionary parameters from pooled next-generation sequencing (NGS) data.

SNPHarvester

• Description : A tool to search for significant SNP groups in large-scale association studies. It can select a set of significant SNP groups from hundreds of thousands of SNPs efficiently.

SNPHunter

• Description : A web tool for dowloading anf management of single nucleotide polymorphism (SNP).

SNPinfo

• Description : A web site with a sute of tools for single nucleotide polymorphism (SNP) detection. For example, SNPs affecting protein structure, gene regulation, slicing, and miRNA binding.

SNPMeta

• Description : SNP annotation and SNP metadata collection of nonmodel species or species that lack a reference genome.

SNPrank

• Description : A tool to rank the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN).

SNPRanker

• Description : A tool for identification and scoring of SNPs.

SNPs3D

• Description : A website with tools for assignng molecular functional effects of non-synonymous single nucleotide polymorphisms (SNPs) based on structures and sequences.

SNPscan

• Description : A web application for the analysis of single nucleotide polymorphism (SNP) Affymetrix array data.

SNPselector

• Description : A web tool for selecting SNPs for genetic association studies.

SNPServer

• Description : A web tool for discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to cluster and align these sequences. The alignments are parsed to autoSNP, a program that detects SNPs and insertion/deletion polymorphisms.

SNPsnap

• Description : A Web server for SNP-based enrichment analysis. It matched SNP sets to calibrate background expectations. The tool identifies sets of randomly drawn SNPs, matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene, and gene density. Annotation database is available for download at the website.

SNPStats

• Description : A web-based tool containing classes of statistical methods, extending snpMatrix package.

SNPSTR

• Description : A database of compound microsatellite-SNP markers.

SNPTools

• Description : SNPTools pipeline comprises tools for SNP analysis in next-generation sequencing data. It has an imputation engine refining raw genotype likelihoods to output high-quality genotypes or haplotypes, designed for genotyping studies of large populations. Features: 1. Addresses low coverage sequencing by using effective base depth (EBD), a nonparametric statistic; 2. A variance-based statistic, resulting in high sensitivity and specificity; 3. Employs a clustering algorithm, BAM-specific binomial mixture modeling (BBMM).

SNPTracker

• Description : Extracts rsID and genomic coordinates of SNPs given any version of rs ID(s).

snpTree

• Description : Single nucleotide polymorphism detection and construction of a phylogenetic tree.

SNPViz

• Description : A tool that finds 3D structures of proteins affected by a given single nucleotide polymorphism (SNP) and displays the affected amino acid in the 3D structure. Requires downloading the human reference genome.

SNP_tools

• Description : Add in for MS Excel. Analysis and conversion of genotype data for MS-Excel. It enhances the ability of MS-Excel for genetic and epidemiological functions, such as the calculation of odds ratio (OR), confidence interval (CI), p-value, and power.

SOP3

• Description : A tool for selection of oligonucleotide primers for single nucleotide polymorphism (SNP) analysis by Pyrosequencing.

SparSNP

• Description : A fast and memory-efficient analysis of all SNPs for phenotype prediction. It also does cross-validation.

SPSmart

• Description : A set of Perl scripts for combining single nucleotide polymorphism (SNP) data from within and between databases.

Stacks

• Description : A pipeline for building loci from short-read sequences to build genetic maps for population genomics and phylogeography. Works with restriction enzyme-based data, such as RAD-seq.

STRait Razor v2s

• Description : A tool for short tandem repeat (STR) analysis. It also contains a database of about 2,500 unique sequences.

StrandScript

• Description : A tool that can convert all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer Illumina array designs.

SurvivalGWAS_Power

• Description : A tool to make power for time to event outcomes over a range of design scenarios and analytical methodologies.

SuSPect

• Description : This tool predicts the likelihood of single amino acid variations to be associated with a disease.

SVScore

• Description : A tool for structural variation impact prediction. SVScore aggregates single nucleotide polymorphism (SNP) pathogenicity scores across genomic intervals.

SWEEP

• Description : Pipeline for filtering allelic SNPs from homeologous SNPs (false positives) in allopolyplod species.

Synthesis-View

• Description : A tool to visualize single nucleotide polymorphism (SNP) data.

SynTView

• Description : Interactive genome viewer for microbial genomes. It provides specialized interconnected views for genome organization and polymorphism data, e.g., SNPs.

Tablet

• Description : A lightweight viewer for next generation sequence assemblies and features, such as single nucleotide polymorphisms (SNPs).

TASSEL

• Description : A tool to evaluate trait associations, linkage disequilibrium, and evolutionary patterns.

TeraPCA

• Description : TeraPCA is a tool for principal component analysis of genomic markers in large genomes. The TeraPCA algorithm can work multi-threaded and requires only a few gigabytes of RAM. TeraPCA requires BLAS and LAPACK libraries.

The UCSC Genome Browser

• Description : The web application provides a radpid display of chosen section of genome sequences and tens of aligned annotation annotation tracks, such as ESTs, mRNAs, CpG islands, known genes, predicted genes, assembly gaps, assembly coverage, chromosomal bands, mouse homologies, and much more. Individual items in the tracks opens details pages and provide direct links to othe repositories, such as OMIM, GenBank, PubMed, Entrez, etc, and much more functionality than it is possible to compress into this short description. The binaries are available for download, allowing you to use it for your own genome. The web app contains sequences of over 100 species, including human (Latest: Human assembly is Dec. 2013 [GRCH38/hg38]).

TIARA genome database

• Description : TIARA genome database contains personal genomic information, such as next generation sequencing (NGS) and ultra-high-resolution comparative genomic hybridization (CGH) arrays. The database allows detection of genomic variations, SNPs, short indels, and structural variants (SVs).

traseR

• Description : An R package to analyze trait associated single nucleotide polymorphism (SNP) enrichment. Visualization of results.

TRES

• Description : Toolbox for ranking and evaluation of SNPs (TRES).

UGbS-Flex

• Description : UGbS-Flex consists of a set of script to combine publicly available software tools for single nucleotide polymorphism (SNP) detection - genotyping by sequencing. The UGbS-Flex pipeline can use paired-end reads as an input.

UPDtool

• Description : A tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments.

VarDetect

• Description : A tool to detect single nucleotide polymorphism in fluorescence chromatograms.

VARIANT

• Description : A tool for functional characterization of variants in next-generation sequencing.

VARiD

• Description : A Hidden Markov Model for SNP and indel identification in AB-SOLiD color-space, and regular letter-space reads.

VarScan

• Description : A tool to detect sequence variants using heuristics / statistics accoring to set thresholds.

VAS

• Description : Web application for Single nucleotide polymorphism (SPN) annotation.

VIRGO

• Description : Visualization and annotation.

Virmid

• Description : A tool to detect impurity and somatic variation, single nucleotide polymorphism (SNP), in somatic tumor sequencing data. The Virmid algorithm uses maximum likelihood estimator (MLE) for the joint probabilities of control and disease genotypes and sample contamination level.

WASP

• Description : Tool to design allele-specific (AS) primers for human SNPs and mutations. Includes a SNP database conprising over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap, and JSNP.

WEP

• Description : Whole-Exome sequencing Pipeline web tool comprising tthe following steps: (1) Read timming, quality checks, filtering, (2) Gapped sequence alignment, (3) BAM conversion, (4), Dublicate removal, (5) Deletion of other artifacts, (6) Calibration of quality scores, (7) SNV and DIP calling, (8) Annotation association, (9) Post processing of data.

WS-SNPs&GO

• Description : A web-based tool for prediction of disease associated SNPs. The method is based on support vector machine (SVM) analyses of proteins.

XSim

• Description : A software tool to simulate sequence data and pedigree structures. User-defined parameters include allele frequencies, map positions, number of loci, chromosome lengths, number of chromosomes, and mutation rates.

XWAS

• Description : A software package to single-marker and gene-based analyses of X chromosome. It can perform various statistical tests, such as the standard test between a single nucleotide polymorphism (SNP) and disease risk, a test for a differential effect of a SNP on disease between males and females, motivated by X-inactivation, a test for higher variance of a trait in heterozygous females as compared with homozygous females, and for all tests, a version that allows for combining evidence from all SNPs across a gene.

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