Genetic NetworksEnvironmentDescriptionKey FeaturesData InputLinkcitation
EDENetworksStandalone GUI built on PythonPopulation and individual-level networks; includes computation of genetic distance matrix, thresholding via percolation point, data visualisation, calculate network metrics and options for data permutations Network creation, analysis and visualisation Allozymes, Microsatellites, AFLP, RFLP, SNPshttps://wwz.ifremer.fr/clonix/Logiciels/EDENetworksKivelä et al. (2015)
NetStruct HierarchyRequires Python and Java JRE to run. Uses Mathematica for network visualisationGenetic relatedness network; calculates between-individual genetic similarity and constructs genetic relatedness network.construct the population structure trees, and conducts community analysis, geographic network visulisation. Requires input as inter-individual genetic
similarity matrix (recommends python tool asd for constructing matrix). Has built in function for SNP data
https://www.greenbaumlab.com/softwareGreenbaum et al. (2019)
NETVIEW PPython initially, transferred to R Population and genetic relatedness networks; Raw data quality control, calculate genetic distance matrix, optional community detection and network visualisationPrimarily for visualisationsymmetrical genetic distance matrixhttps://github.com/esteinig/netviewSteinig et al. (2016)
PopgraphRPopulation networks; builds population networks based on Dyer and Nason (2004) and draws on igraph (R) to plot and analysis network metricsPopulation network visualisation (spatial) and analysisMatrix of genetic covariance (Dryer et al. 2004) from r package gstudiohttps://github.com/dyerlab/popgraphDyer (2014)
robinRValidation of community detection methods; examines the robustness of a community detection method and compares between different community detection algortihms - built to implement igraph community detection algorithms.Statistical significance of network communities, and comparison of community algorithms A genetic network in the form of an igraph objecthttps://cran.r-project.org/web/packages/robin/index.htmlPolicastro et al. 2021
Genetic Distance and RelatednessEnvironmentDescriptionKey FeaturesData InputLinkcitation
COANCESTRYStandalone Windows GUI, Fortran source Genetic relatedness networks; Calculates 7 relatedness measures and 4 inbreeding metricsPairwise relatedness, inbreeding coefficients, comparing population inbreeding levels via bootstrapping, genotype simulations, Multilocus genotype data (ie. Microsatellite, SNPs)https://www.zsl.org/science/software/coancestryWang (2011)
COLONYStandalone Windows GUI, Mac and Linux, and available R implementation (rcolony) Pedigree networks; Implements maximum likelihood analysis to estimate parentage and siblingshipEstimates parents, full-siblings and half-siblings. Can detect and account for typing errors and mutations. Handles diploid and haplo-diploid dioecious and diploid monoecious with selfing. Inferance of parent genotypes.Multilocus genotype data (ie. Microsatellite, SNPs)https://www.zsl.org/science/software/colonyJones & Wang (2010)
FRANzStandalone program available on Windows, Mac and Linux Pedigree networks; Pedigree reconstruction for wild populations with Markov Chain Monte Carlo, can incorporate prior information (i.e. known relationships)Estimates parents and full-siblings. Can incorperate prior knowledge (sex, age, sub-pedigree, siblings, location). Accounts for typing errors and mutations. Multilocus genotype data (ie. Microsatellite, SNPs)http://www.bioinf.uni-leipzig.de/Software/FRANz/About.htmlRiester et al. (2009)
gstudioRSpatial analysis of population genetic data, builds covariance matrices as described in Dryer et al. 2004. Spatially plotting population data, constructing genetic covariance matrices (for popgraph)Multilocus genotype data (ie. Microsatellite, SNPs)https://github.com/dyerlab/gstudioDyer (2014)
MEMGENERUses regression framework to analyse spatial genetic data and generate Moran's eigenvectors maps, detect and visualize spatial genetic patternsUses Moran's Eigenvector Maps (MEM) to extract only the spatial component of genetic variationgenetic distance matrixhttps://cran.r-project.org/web/packages/memgene/index.htmlGalpern et al. (2014)
ML-relateStandalone program available on WindowsGenetic relatedness networks; calculates maximum likelihood analysis to estimate between individual relatednesscreates maximum likelihood estimates of relatedness & can categories as parent-offspring, full-sib, half-sib and unrelatedmicrosatellite data (in GENEPOP formats)https://www.montana.edu/kalinowski/software/ml-relate/index.htmlKalinowski et al. (2006)
relatedRR implementation based on COANCESTRY. Computes 7 relatedness metrics and includes additional simulation functions to determine how each measure performs given the specific dataPairwise relatedness, inbreeding coefficients, comparing population inbreeding levels via bootstrapping, genotype simulations, Multilocus genotype data (ie. Microsatellite, SNPs)https://github.com/timothyfrasier/relatedPew et al. (2015)
SPAGeDiStandalone program available on Windows, Mac and LinuxPopulation and genetic relatedness; methods for calculating genetic distances between populations (i.e. FST, RST) and multiple kinship, relatedness and fraternity relationships at the individual level Can handle spatial and non-spatial analysis. Computes population statistics (i.e. Fst, Rst, Nst, Ds) and pairwise relatedness and kinship estimators. Built in permutations to asses spatial structure, population differentiation and inbreedinggenotype data of any ploidy levelhttps://ebe.ulb.ac.be/ebe/SPAGeDi.htmlHardy & Vekemans (2002)
General NetworkEnvironmentDescriptionKey FeaturesData InputLinkcitation
igraphR, python and C versions Flexible network analysis for building networks from adjacency matrices or edge lists, calculating a wide breadth of network metrics and community detection algorithms, visualising networks and performing some network permutations Build, analyses and visualize networks network matrix or edge listhttps://igraph.org/Csardi & Nepusz (2006)
MuxVizR implemented with a GUIComputes multilayer network metrics and statistics as well as multilayer network visualisationCreates multilayer networks, calculates multilayer statistics (ie. Edge overlap, multilayer community detection, edge list for each layer and file containing information on each layerhttps://manlius.github.io/muxViz/index.htmlDe Domenico et al. (2015)
snaR packageBuild, analsyse and graph networks. Calculates a breadth of general network metrics and community analysis. Functions for random graph generation for null models. Build, analyses and visualize networks network matrix or edge listhttps://cran.r-project.org/web/packages/sna/index.htmlButts (2020)
gephiStandalone program (windows, linux, mac)Visulaize networks and network explorationsReal-time visualization of networks, basic networks statistics Edgelisthttps://gephi.org/Bastian et al. (2009)

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