PopSim

Segment(start::T, stop::T)

A genomic segment defined by its start and stop positions. The start and end positions are inclusive.

StationaryPopulation(ploidy::Int, size::Int)

A simple demography for population modeling.
A stationary population with a fixed ploidy and size.

UniformRate(rate::Float64)

A uniform rate distribution for genetic processes.

VaryingPopulation(; ploidy = 2, population_sizes = [1_000], times = [0.0],
genome_length = 1_000_000, recombination_rate = 1.0e-8, mutation_rate = 1.0e-8)

Create a varying population with the given parameters.

Arguments

• ploidy::Int: The ploidy of the population. Default is 2.
• genome_length::Int: The length of the genome. Default is 1000000.
• recombination_rate::Float64: The recombination rate. Default is 1.0e-8.
• mutation_rate::Float64: The mutation rate. Default is 1.0e-8.
• population_sizes::Vector{Int}: The sizes of the population at different times. Default is [1_000].
• times::Vector{Float64}: The times at which the population sizes are specified. Default is [0.0].

Notes

• The population sizes and times must have the same length.
• The times must be sorted in ascending order.
• The first time must be 0.0.

Example

To model a population which starts at N=1000, goes throw a bottleneck (N=200) from 150 genertions ago to 120 generations ago and then recovers to N=2000 individuals, you can use the following:

times = [0.0, 120.0, 150.0]
population_sizes = [2000, 200, 1000]