CurrentModule = 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.
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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:
Pages = [
"man/getting_started.md",
"man/mapping_genetree_to_network.md",
"man/converting_coal2generation_units.md",
"man/correlated_inheritance.md",
"man/more_examples.md",
]
Depth = 3
For help on individual functions, see the library:
Pages = [
"lib/public.md",
"lib/internal.md",
]
Depth = 3