A phylogeny is a tree or a network that describes the past history of a group of organisms (individuals, populations, species; also languages). A node represents a splitting event, such as a population divergence or speciation; or a merging event, such as from hybridization, introgression, gene flow or admixture.
Research in evolutionary biology uses phylogenetics (or phylogenomics) to infer phylogenies from molecular sequence data, and use these phylogenies for the discovery of evolutionary patterns about trait evolution, diversification, etc.
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There are a variety of Julia packages built by JuliaPhylo contributors. Most of them rely on the core PhyloNetworks package.
SNaQ is a package for inferring level-1 phylogenetic networks from quartet concordance factors.
SNaQ implements a statistical method for inferring level-1, semi-directed phylogenetic networks from quartet concordance factors. The approach heuristically searches phylogenetic network space while optimizing branch lengths based on the quartet concordance factors that are expected under the network multispecies coalescent model. The use of quartet concordance factors and pseudolikelihood make SNaQ an accurate and more scalable alternative to traditional model-based phylogenetic network inference methods such as full-likelihood or Bayesian methods.
PhyloTraits is a package for trait evolution along phylogenies.
PhyloTraits provides functions for simulating and analyzing the evolution of both continuous and discrete
traits
along phylogenies, including phylogenetic networks. PhyloTraits enables researchers to test various
hypotheses of trait evolution by
fitting many models to character data on a phylogeny.
This package also allows users to estimate rates of evolution,
ancestral states,
and assess the correlation between multiple traits.
PhyloCoalSimulations is a package to simulate phylogenies under the coalescent. It implements the network multi-species coalescent model with possible inheritance correlation.
PhyloPlots has utilities to plot tree and network objects from PhyloNetworks through R via RCall.
QuartetNetworkGoodnessFit, aka "Quarnet GoF" or simply "QGoF", is a package for phylogenetic networks analyses using four-taxon subsets. It includes tools to measure the goodness of fit of a phylogenetic network to data on subsets of 4 tips.
PhyloGaussianBeliefProp, or simply "PGBP", is a package for the analysis of Gaussian models on phylogenetic networks and admixture graphs using belief propagation (aka message passing).
Here are other resources, such as non-Julia repositories and outside tutorials:
