SNP
- Section 26 – Software Suite for Parsimonious Recombination Analysis of SNP data
- GenABEL 1.7-4 – Genome-wide SNP Association Analysis
- Biofilter 2.0.0 rc 2 – Knowledge-driven Multi-SNP analysis of large scale SNP data
- SNPAssoc 1.8-5 – SNPs-based Whole Genome Association Studies
- FastTagger 1.0 – Genome-Wide Tag SNP selection
- MACLEAPS 0.5 – Machine Learning Analysis Pipeline for Genome-Wide Accociation Study SNP data
- PEAS 1.0 – Package for Elementary Analysis of SNP data
- SNPscan – Affymetrix SNP (10K, 50K, 100K, 500K) Visualization
- SNPduo 1.02a – Pairwise Comparisons of SNP data sets
- pediSNP – Locate Meiotic Recombination Sites from SNPs
- kcoeff – Calculate Genetic Relatedness from SNP data
- SparSNP – Fit Lasso-penalized linear models to SNP data
- Tagger – Selection and Evaluation of tag SNPs
- SNEASER 1.0 – SNP Filter pipeline
- LDheatmap 0.99 – Graphical Display of Pairwise Linkage Disequilibria between SNPs
- hapassoc 1.2-6 – Inference of Trait Associations with SNP Haplotypes and other attributes using the EM Algorithm
- QCTOOL 1.3 – SNP Quality Control (QC) for Genome-wide Association Studies
- shellfish – Parallel PCA and data processing for Genome-wide SNP data
- McSNP 1.0 – Melting Curve SNP
- AGSNP 1.2 – Annotation-based, Genome-wide SNP Discovery
- PolyScan 3.0 – Automatic Indel and SNP Detection
- SATlotyper 0.1.5 – Haplotype Inference from unphased SNP data in Heterozygous Polyploids based on SAT
- dChip 2011.12 – Analysis & Visualization of Gene Expression & SNP Microarrays
- SnpStore 1.0 – SNP and Indel Calling in mapped NGS Sequencing Reads
- FaSD – Fast SNP Detector
- Syzygy 1.2.7 – SNP and Indel Calling for pooled and individual Targeted Resequencing Studies
- PS_SNP – Prioritize and Select SNPs for Whole Genome Association Studies with Two-stage Designs
- Admixture 1.22 – Maximum Likelihood Estimation of Individual Ancestry based on Multilocus SNP Genotypes
- csnpAnalysis 1.02 – PANTHER Coding SNP Analysis tool
- AffyMAPSDetector 1.0 – Affymetrix MicroArray Probe SNP Detector
- SNPTrack 1.1.0 – SNP & GWAS Data Management, Analysis and Interpretation
- GenoSNP 1.3 – SNP Genotyping
- SNP2CAPS – SNP and INDEL Analysis Tool for CAPS Marker Development
- SNPPIT 1.0 – Perform Fast and Accurate, Likelihood-based, Parentage Inference with SNPs
- SNPLINK – Multipoint Linkage analysis of Densely Distributed SNP data
- SNP HiTLink 1.5.1 – SNP High-Throughput Linkage Analysis System
- SNPALYZE 8.0 – SNP and Disease Association Analysis Software
- SNaP – Simulation of sNp haplotype data And Phenotypic traits
- snp.plotter 0.2.1 – SNP/haplotype Association and Linkage Disequilibrium plotting package
- Synthesis-View – Visualization and Interpretation of SNP Association Results
- SNPEVG 2.1 – SNP Effect Viewing and Graphing
- ldgroup – Linkage Disequilibrium Grouping of SNPs
- INTERSNP 1.0.10 – Genome-wide Association and INTERaction Analysis of SNP
- SSEA 1.0 – SNP Set Enrichment Analysis for Genome-wide Association Studies
- GEC 1.0 – Address Multiple-testing Issue with dependent SNPs
- mPopTag – Multi-Population Tag SNP Picker
- SNPdetector 20051014- Sensitive and Accurate SNP Detection
- AsVis 20051125 – Visualizing Association Rules in SNP Neighborhoods
- Clarki 20090715 – Use SNP data for Species Identification
- SNPHAP 1.3.1 – Estimate Frequencies of Haplotypes of SNPs
- CLUSTAG – Hierarchical Clustering and Graph Methods for Selecting Tag SNPs
- ATRIUM 1.0 – Testing Untyped SNPs in Case-Control Association Studies with Related Individuals
- MegaSNPHunter – Detect Disease Predisposition SNPs and High Level Interactions
- SNPCaller – Smarter Clustering Methods for SNP Genotype Calling
- Polymorfind 0.1 – SNPs and Indels Detection
- CNVEM 0.710 – Infer Carrier Status of CNVs in Large Samples from SNP Genotyping Data
- AssociationViewer 2.0 – Display SNPs in Genetic Context
- SNP-HWE – Routines for exact SNP tests of Hardy-Weinberg Equilibrium
- PUS-POPPIN’ FROGS 1.01 – Determine each Frog’s SNP Profile, Test the Drugs Game
- GenePool 0.9.1 – Analyze SNP Microarray Probe Intensity data & Rank SNPs
- SWAP454 1.2 – Call SNPs using 454 Read Data
- PolyPhred 6.18 – SNP Detection
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