PhyloCoalSimulations

PhyloCoalSimulations is a Julia package to simulate phylogenies under the coalescent. It depends on PhyloNetworks for the phylogenetic data structures, and manipulation of phylogenies.

References: please see bibtex entries here.

• for this package and the network coalescent model with inheritance correlation:
  Fogg, Allman & Ané (2023). PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow. Systematic Biology, 72(5):1171–1179. doi:10.1093/sysbio/syad030.

• for PhyloNetworks, which this package depends on:
  Solís-Lemus, Bastide & Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution, 34(12):3292–3298. doi:10.1093/molbev/msx235

For a tutorial, see the manual:

• getting started
• • installation
  • basic simulation example
  • • example network
    • basic example: simulate, save to file, plot
  • several individuals per species
• mapping gene trees into the species phylogeny
• • naming internal nodes
  • mapping gene tree edges back into species edges
  • cleaning gene trees
• converting between units
• • converting edge lengths in gene trees
• number of generations in the network and gene trees
• correlated inheritance
• example uses
• • counting deep coalescences
  • number of lineages inherited via gene flow
  • rate variation across species

For help on individual functions, see the library:

• public documentation
• • functions & types
  • index
• internal documentation
• • functions & types
  • index