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SERAPHIM / Studying Environmental Rasters and PHylogenetically Informed Movements
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.
SPREAD / Spatial Phylogenetic Reconstruction of Evolutionary Dynamics
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.
GeoSymbio
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.
Ginkgo
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.
SPAGeDi / Spatial Pattern Analysis of Genetic Diversity
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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.
PDA / Phylogenetic Diversity Analyzer
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.
Treelink
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.
T2prhd / tree to pairwise repeat homology diagram
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.
Biodiverse
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.
GeoAssign
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.
Conserve IV
Assesses and prioritizes conservation schemes based on phylogenies. While it would be best to preserve all species and populations, in the management of biodiversity it is often necessary to perform a triage. Decisions must be made as to which populations, species and habitats should be given the highest priority. Other things being equal, these priorities should be set on the basis of evolutionary distinctiveness, and Conserve enables you to do this using genetic distances and also to test whether particular assemblages of populations preserve statistically significantly more biodiversity than other assemblages.
PHYLOSCANNER
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.
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