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Haplotype network inference software tools | Population genomics

Haplotype networks are used in the analysis of population genetic data to visualise genealogical relationships at the intraspecific level, as well as to make inference about biogeography and history of populations.Source text:(Leigh and Bryant,…
PopGenome
Desktop

PopGenome

A population genomics package for the R software environment (a de facto…

A population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual…

PopART
Desktop

PopART Population Analysis with Reticulate Trees

An integrated software package that provides a comprehensive implementation of…

An integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with…

adegenet
Desktop

adegenet

An R package dedicated to the multivariate analysis of genetic markers.…

An R package dedicated to the multivariate analysis of genetic markers. adegenet extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and…

Fitchi
Desktop

Fitchi

A program that produces publication-ready haplotype genealogy graphs. Fitchi…

A program that produces publication-ready haplotype genealogy graphs. Fitchi uses reticulation-free phylogenetic trees and the Fitch algorithm to reconstruct haplotype genealogies. Haplotype…

Arlequin
Desktop

Arlequin

A software package integrating several basic and advanced methods for…

A software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and…

AveDissR
Desktop

AveDissR

Integrates three separate analyses of the average dissimilarity (AD) approach.…

Integrates three separate analyses of the average dissimilarity (AD) approach. AveDissR identifies genetically distinct or redundant germplasm. It takes in consideration five different data types of…

pegas
Desktop

pegas Population and Evolutionary Genetics Analysis System

A package for the analysis of population genetic data. pegas provides functions…

A package for the analysis of population genetic data. pegas provides functions for standard population genetic methods, as well as low-level functions for developing new methods. The flexible and…

GenAlEx
Desktop

GenAlEx Genetic Analysis in Excel

A cross-platform package for population genetic analyses that runs within…

A cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both…

HapStar
Desktop

HapStar

A tool for viewing haplotype networks and minimum spanning networks. HapStar is…

A tool for viewing haplotype networks and minimum spanning networks. HapStar is unique in that it automatically lays out the network for optimal visualisation, and provides the option to calculate a…

PGEToolbox
Desktop

PGEToolbox

A powerful and flexible Matlab toolbox dedicated to the analysis of DNA…

A powerful and flexible Matlab toolbox dedicated to the analysis of DNA sequence polymorphisms and SNPs. The main features of PGEToolbox are as follows: 1) capability for handling both DNA sequence…

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