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 suite of computational methods developed to study phylogenetic reconstructions of spatial movement in an environmental context. SERAPHIM extracts the spatio-temporal information contained in estimated phylogenetic trees and uses this information to calculate summary statistics of spatial spread and to visualize dispersal history. Most importantly, SERAPHIM enables users to study the impact of customized environmental variables on the spread of the study organism. Specifically, given an environmental raster, SERAPHIM computes environmental “weights” for each phylogeny branch, which represent the degree to which the environmental variable impedes (or facilitates) lineage movement. Correlations between movement duration and these environmental weights are then assessed, and the statistical significances of these correlations are evaluated using null distributions generated by a randomization procedure. SERAPHIM can be applied to any phylogeny whose nodes are annotated with spatial and temporal information.
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.
A user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial-temporal diffusion. The software maps phylogenies annotated with both discrete and continuous spatial information and can export high-dimensional posterior summaries to keyhole markup language (KML) for animation of the spatial diffusion through time in virtual globe software. In addition, SPREAD implements Bayes factor calculation to evaluate the support for hypotheses of historical diffusion among pairs of discrete locations based on Bayesian stochastic search variable selection estimates. SPREAD takes advantage of multicore architectures to process large joint posterior distributions of phylogenies and their spatial diffusion and produces visualizations as compelling and interpretable statistical summaries for the different spatial projections.
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.
A web based application that plots any sort of frequency data with a geographic component. PhyloGeoViz was designed to create geographic visualizations of DNA haplotype data that are often used in the course of phylogeographic analysis. These visualizations demonstrate the spatial distributions of each haplotype, the frequency of each haplotype in each population, and the number of samples included per population. However, the program can be used for any kind of data.
A package for agent-based, forward-time simulations of genealogies of multiple unlinked loci from diploid populations. Ginkgo simulates the evolution of one or more species on a spatially explicit landscape of cells. The geographical elements modelled include the arrangement of cells and movement rates between particular cells. Each species has a function that can calculate a fitness score for any combination of an individual organism’s phenotype and environmental characteristics. In addition to their differing fitness functions, species can differ in terms of their vagility and fecundity. Genealogies and occurrence data can be produced at any time during the simulation.
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.
A web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network. Taking advantage of modern graphic libraries, tcsBU also improves the speed at which the final network layout is reached. Networks can be saved as a Scalable Vector Graphics format.
Identifies pairwise local gap-free alignments where pairs of identical nucleotides are aligned to each other at certain, pre-defined positions, while mismatches are possible elsewhere. FSWM is an alternative alignment-free approach to estimate phylogenetic distances between large genomic sequences. FSWM is able to rapidly detect homologies among genomic sequences, as a basis for phylogeny reconstruction.
Allows exploration of large phylogenetics trees in an epidemiological context. PhyloGeoTool is an application to interactively navigate large phylogenies and to explore associated clinical and epidemiological data. The software implements an algorithm that automatically partitions a phylogeny into an optimal number of clusters, thereby recursively partitioning each identified cluster. The interface provides a visualization of the initial tree of clusters.
A fully probabilistic approach for the joint reconstruction of phylogenies and epidemiological parameters, given structured host and/or pathogen populations, based on a multitype birth–death model. BDMM is general to both geographic and nongeographic (e.g., risk group) partitioning. The method is implemented as a package within the widely used Bayesian inference framework BEAST 2, which makes it accessible to a wide audience.
Provides a wide range of biodiversity analysis using Phylogenetic Diversity (PD), Split Diversity (SD) and related measures based on both phylogenetic trees and networks. PDA provides conservation biologists with an objective decision-making process. The major features include: (i) maximizing PD and SD given various types of constraints including budgetary, geographical,and ecological constraints, and (ii) minimizing budget given diversity threshold; evaluation of predefined sets of taxa (e.g. in an area) including exclusive, endemic, and complementary PD/SD.
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 platform-independent software for linking datasets and sequence files to phylogenetic trees. Treelink allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Treelink can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree.
Generates simple diagrams that highlight relationships of sequence repeats detected by using a profile Hidden Markov Model (HMM) in two sequences. t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families), as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of scripts.
A tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix (e.g. genetic dissimilarity) relationships. The explosion in georeferenced biological specimen and survey data means there is an increasing need for such tools. Biodiverse supports four processes: 1) linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces; 2) spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity; 3) spatially constrained agglomerative cluster analyses; and 4) randomisations for hypothesis testing. Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface and scripts.
Allows users to quantify and visualize gradients of genetic variation with the aim to pinpoint possible origin of expansion. ‘Genetic hubs’ is a method that estimates local genetic variability as an accessibility of all genetic variation from the site in question and it allows to take dissimilarity of genotypes into account. This application can be used for exploratory analyses of various kinds of genetic data, including those as typical in mitochondrial phylogeography.
Assigns test individuals according to their genotypes or metric traits to groups (e.g. country of origin, population of origin) which are defined by reference individuals. GeoAssign uses a nearest neighbour classification approach that assigns unclassified individuals to predefined classes of reference individuals, such as by the country of origin that is of relevance for the timber trade or any CITES listed species with different country restrictions. The distance between individuals is measured by the genic distance between their multilocus genotypes, defining the nearest neighbours of a specific individual as those individuals with the smallest genic distance to it.