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Genetic Analysis: GWAS Genetic Variation Linkage Analysis Gene Expression
Sequence Analysis: Assembly Annotation Alignment RNAi RNA-seq Primer Design Next Generation Tools Phylogenetic Analysis Gene Structure Viral
The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform.
EIGENSTRAT detects and corrects for population stratification in genome-wide association studies using principal components analysis.
GeneHunter is a tool for rapid extraction of complete multipoint linkage analysis using both parametric and nonparametric approaches.
The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.
GRAIL is an algorithm to assess biological relationships between disease-associated genetic variants.
Haploview is designed to facilitate the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
InVEx (Introns Vs Exons) is a permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer genomics studies, with particular relevance to high mutation rate cancers. Mutations are permuted on a per-patient, per-trinucleotide-context basis across the exons, introns and UTRs of a gene, generating a null model of the distribution of mutations to which the observed distribution can be compared to determine statistical significance. Significant genes are of interest, as their somatic mutation is likely to be important in the formation of the cancer being studied. The method can operate on whole exome as well as whole genome sequencing data.
LocusView is a program for generating images of chromosomal regions annotated with genomic features, experimental data, and analysis results.
MAGENTA is a program that tests whether predefined biological processes or gene sets are enriched for genes associated with a complex disease or trait.
MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.