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Showing 8 records out of 8 total

Categories: population genetics - Software type(s): CLI, GUI - tool
Arlequin provides the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. One can explore the data, and analyze several times the same data set from different perspectives, with different selected options.
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
Categories: genomics, evolutionary biology, population genetics - Software type(s): CLI, GUI - tool
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.
Categories: genomics - Software type(s): CLI - tool
FastEpistasis is a high performance tool designed to test for epistasis effects when analysing continuous phenotypes. It computes tests of epistasis for a large number of SNP pairs, and is an efficient parallel extension to the PLINK epistasis module.
Categories: genomics, (characterisation/annotation) - Software type(s): CLI - tool
Gaussian Mixture Model (GMM) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).
Categories: genomics - Software type(s): website - database/tool
The resource is based on a new 'in silico' approach for identifying regulatory variants. The transcription factor (TF) binding score is computed in both the reference (hg19) and alternate human genome assemblies. The alternate genome assembly is generated by incorporating the alternate allele of common genetic variants (AF>=0.001) from the 1000 Genomes Project. Interesting candidate variants are those SNPs that disrupt, create or change the TF binding score/affinity between the two genomes.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
SwissVar is a portal to search variants (polymorphism) in UniProt Knowledgebase (UniProtKB) entries, and gives direct access to manual annotation on the genotype-phenotype relationship of each specific variant based on literature, as well as pre-computed information (such as conservation scores and a list of structural features when available) to help assess the effect of the variant.
Categories: genomics, (sequence alignment), population genetics - Software type(s): CLI - tool
V-pipe is a bioinformatics pipeline for the analysis of next-generation sequencing (NGS) data derived from intra-host viral populations.