Haplotype visualization software tools | Population genomics
Haplotype reconstruction is an important tool for understanding the aetiology of human disease. Haplotyping infers the most likely phase of observed genotypes conditional on constraints imposed by the genotypes of other pedigree members. The results of haplotype reconstruction, when visualised appropriately, show which alleles are identical by descent despite the presence of untyped individuals. When used in concert with linkage analysis, haplotyping can help delineate a locus of interest and provide a succinct explanation for the transmission of the trait locus.
A pedigree-drawing application with special features for easy visualization of complex haplotype information. HaploPainter has been developed to facilitate gene mapping in mendelian diseases in terms of fast and reliable definition of the smallest critical interval harbouring the underlying gene defect. Features like haplotype compression and the ability of marker section cut-out are particularly helpful for viewing large SNP-derived haplotypes.
Permits users to visualize marker data from biparental populations. ABHgenotypeR can be useful for analyzing and presenting genotypes in the ABH format. It includes some modules to correct short miscalled stretches or under-called heterozygous sites based on flanking alleles, to plot the parental allele frequencies along the chromosomes, or to plot the marker density along the chromosomes.
Allows visualization of the haplotype cluster frequencies produced by statistical models for population haplotype variation. Haploscope enables flexible renderings of model features directly produced by the statistical model for haplotype structure implemented in fastPHASE and also from other cluster-based models for haplotypes in populations. The software allows various options for generating images and provides investigators with the ability to report visually appealing and informative plots of haplotype structure.
Dissects a reasonable fraction proteins into domain-like fragments. CHOP uses the minimal coverage of a known domain and the minimal level of sequence similarity. The tool contains three hierarchical steps that were applied by decreasing confidence in the accuracy of the information. The main limitation of the tool is that it failed to identify all domain boundaries: 31% of the proteins remained unchopped; these accounted for 15% of all final CHOP fragments.
Provides an interface for visualizing unphased genotypes and phased haplotypes. inPHAP is an interactive application allowing users to investigate patterns in large genetic datasets and to study influences of variants on both individual and general level. It includes a wide range of features organized according six panels that allows users, for instance, to display data or to summarize general information for the loaded data set.