Phylogeography aims to relate evolutionary processes to spatial, temporal and environmental factors in order to understand past and present biodiversity (Avise et al., 1987; Hickerson et al., 2010; Kidd and Liu, 2008). Source text: Parks et al., 2013.

Web app
GeoAssign GeoAssign

GeoAssign

Assigns test individuals according to their genotypes or metric traits to…

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…

Desktop app
Ginkgo Ginkgo

Ginkgo

A package for agent-based, forward-time simulations of genealogies of multiple…

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…

Web app
Desktop app
Phylogenetic… Phylogenetic Diversity Analyzer

PDA Phylogenetic Diversity Analyzer

Provides a wide range of biodiversity analysis using Phylogenetic Diversity…

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…

Desktop app
Studying… Studying Environmental Rasters and…

SERAPHIM Studying Environmental Rasters and PHylogenetically Informed Movements

A suite of computational methods developed to study phylogenetic…

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…

Desktop app
Bayesian Analysis of… Bayesian Analysis of Population Structure

BAPS Bayesian Analysis of Population Structure

A program for Bayesian inference of the genetic structure in a population. BAPS…

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…

Web app
Treelink Treelink

Treelink

A platform-independent software for linking datasets and sequence files to…

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…

Web app
Desktop app
Filtered Spaced Word… Filtered Spaced Word Matches

FSWM Filtered Spaced Word Matches

Identifies pairwise local gap-free alignments where pairs of identical…

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…

Desktop app
tree to pairwise… tree to pairwise repeat homology diagram

T2prhd tree to pairwise repeat homology diagram

Generates simple diagrams that highlight relationships of sequence repeats…

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…

Desktop app
Conserve IV Conserve IV

Conserve IV

Assesses and prioritizes conservation schemes based on phylogenies. While it…

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…

Desktop app
Reconstruct Ancestral… Reconstruct Ancestral State in Phylogenies

RASP Reconstruct Ancestral State in Phylogenies

Infers historical biogeography through reconstructing ancestral geographic…

Infers historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees. RASP utilizes the widely used Statistical-Dispersal Vicariance Analysis (S-DIVA), the…

Desktop app
BDMM BDMM

BDMM

A fully probabilistic approach for the joint reconstruction of phylogenies and…

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.…

Web app
tcsBU tcsBU

tcsBU

A web-based program that extends the capabilities of TCS, by implementing…

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…

Desktop app
Biodiverse Biodiverse

Biodiverse

A tool for the spatial analysis of diversity using indices based on taxonomic,…

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…

Desktop app
DIVA-GIS DIVA-GIS

DIVA-GIS

A free computer program for mapping and geographic data analysis (a geographic…

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…

Web app
PhyloGeoViz PhyloGeoViz

PhyloGeoViz

A web based application that plots any sort of frequency data with a geographic…

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…

Desktop app
Spatial Phylogenetic… Spatial Phylogenetic Reconstruction of…

SPREAD Spatial Phylogenetic Reconstruction of Evolutionary Dynamics

A user-friendly, cross-platform application to analyze and visualize Bayesian…

A user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial-temporal diffusion. The software maps phylogenies annotated with…

Desktop app
Web app
Phylowood Phylowood

Phylowood

A web app that uses JavaScript to generate in-browser animations of…

A web app that uses JavaScript to generate in-browser animations of biogeographic and phylogeographic histories from annotated phylogenetic input. The animations are interactive, allowing the user to…

Desktop app
GenGIS GenGIS

GenGIS

A bioinformatics application that allows users to combine digital map data with…

A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS (pronounced 'Genghis' like…

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