Geospatial inference software tools | Population genetics data analysis
Large-scale genotype datasets can help track the dispersal patterns of epidemiological outbreaks and predict the geographic origins of individuals. Such genetically-based geographic assignments also show a range of possible applications in forensics for profiling both victims and criminals, and in wildlife management, where poaching hotspot areas can be located. They, however, require fast and accurate statistical methods to handle the growing amount of genetic information made available from genotype arrays and next-generation sequencing technologies.
Provides a statistical platform for the evaluation of the relationship between genetic and geographic distance. IBDWS processes genetic data with or without corresponding geographical information. This software can analyze raw data with codominant markers and perform statistical tests like Mantel tests or reduced major axis regression of isolation by distance (IBD). It can also find statistically significant relationship between the genetic distance matrix and the comparable matrix of geographic distance.
Allows simultaneous investigation on interindividual spatial and genetic data. AIS provides a set of methods, applicable to phylogeographical studies, able to both highlight and qualify patterns of spatial genetic structure in a given spatial scale. It offers approaches such as Mantel tests or allelic aggregation index analyses (AAIA) coupled to an utility for generating graphical representations of genetic distance patterns across landscapes.
Implements a Bayesian statistical method for estimating allele frequencies and assigning samples of unknown (or known) origin across a continuous range of locations, based on genotypes collected at distinct sampling locations. In brief, the idea is to assume that allele frequencies vary smoothly in the study region, so allele frequencies are estimated at any given location using observed genotypes at near-by sampling locations, with data at the nearest sampling locations being given greatest weight.
An interactive visualization tool for rapidly displaying the geographic distribution of genetic variants. Through a REST API and dynamic front-end, the GGV browser provides maps of allele frequencies in populations distributed across the globe. After a query, the GGV displays the allele frequencies as a collection of pie charts where each represents the frequency of the globally minor allele in a single population.
Allows investigators to create or upload pictures of their study site, loads diversity analyses data and displays both diversity and taxonomy results in a spatial context. SitePainter includes: visualizing α-diversity, using taxonomic summaries; visualizing β-diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. The features of the tool facilitate fast exploratory analyses of spatial data.
Provides a method to predict an individual's ancestry or DNA use. SPAMIX was developed to preview the geographical origins of multiple recent ancestors for individuals with recent mixed ancestry. It leverages the spatial structure of genetic variation, using hidden Markov models (HMMs) for the admixture process to achieve accuracy in localizing the recent ancestry of a given individual on a geographical map.
A statistical method for geopositioning individuals of unknown origin from genotypes. SPASIBA is based on a geostatistical model trained with a dataset of georeferenced genotypes. Statistical inference under this model can be implemented within the theoretical framework of integrated nested Laplace approximation, which represents one of the major recent breakthroughs in statistics, as it does not require Monte Carlo simulations.