A program for Bayesian inference of the genetic structure in a population. BAPS treats both allele frequencies of the molecular markers (or nucleotide frequencies for DNA sequence data) and the number of genetically diverged groups in population as random variables. However, analyses and model comparisons can also be performed using a fixed number of genetically diverged groups or pre-specified population structures.
A free computer program for mapping and geographic data analysis (a geographic information system). With DIVA-GIS you can make maps of the world, or of a very small area, using, for example, state boundaries, rivers, a satellite image, and the locations of sites where an animal species was observed. DIVA-GIS is particularly useful for mapping and analyzing biodiversity data, such as the distribution of species, or other 'point-distributions'.
Estimates genetic distances between populations or relatedness coefficients between individuals using data from codominant genetic markers. SPAGeDi characterizes association between genetic and spatial distances, permitting investigation of isolation by distance processes. It can find major applications in studies focusing: on sibship genetic structure, genetic differentiation in the case of autopoly-ploids, marker based inference of quantitative inheritance, or phylogeny reconstruction of populations.
Infers historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees. RASP utilizes the widely used Statistical-Dispersal Vicariance Analysis (S-DIVA), the Dispersal–Extinction–Cladogenesis (DEC) model (Lagrange), a Statistical DEC model (S-DEC) and BayArea. It provides a graphical user interface to implement new algorithms for biogeographic inference and integrate more third party tools.
A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS (pronounced 'Genghis' like Genghis Khan) provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.
Allows analysis of pathogen diversity. PHYLOSCANNER is a set of methods that aims to compute phylogenies with multiple genotypes per infected host. It allows users to study inference of biologically and epidemiologically relevant properties from a set of related phylogenies. It performs automatically quantification of within-host diversity, identification of multiple infections, identification of crossover recombination breakpoints in next-generation sequencing (NGS) genotypes, or ancestral host-state reconstruction from multiple phylogenies.
Provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium-host symbioses. GeoSymbio proposes a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or ‘in the cloud’ using Google Apps, and therefore does not require any specialty geographic information systems (GIS), web programming or data programming expertise from the user. GeoSymbio utilizes Symbiodinium data based on the internal transcribed space 2 (ITS2) genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982–2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis.