Distributions

This structure implements a Distribution whos likelihood is calculated
according to Felsensteins algorithm.

function PhyloDist(my_tree::T, base_freq::S, substitution_rates::R, rates::R, substitution_model::Function) where {T<:GeneralNode, S<:DenseArray{Float64}, R<:Real}

Convenience function which can work with MCPhylo types.

generate_constraints!(constraints::ConstraintDict, filename::String)

Function that adds further constraints to an existing dictionary of constraints, based on a txt file with a specific format (each line one constraint). See basic generate_constraints function on a file for more info.

generate_constraints!(
    constraints::Dict;
    mono::Vector{Vector{S}}=Vector{String}[],
    not_mono::Vector{Vector{S}}=Vector{String}[],
    exc::Vector{Tuple{Vector{S}, Vector{S}}}=Vector{Tuple{Vector{String}, Vector{String}}}[]
)::ConstraintDict where S<:AbstractString

Function that adds further constraints to an existing dictionary of constraints. See basic generate_constraints function for more info.

generate_constraints(filename::String)

Function that creates a dictionary of constraints, based on a txt file with a specific format, i.e.:

lines starting with '#' will be ignored

multiple constraints per line allowed

mono: A,B; C,D; mono: E,F;

final semicolon is optional

not_mono: C,D,E exc : E,F!G;

See basic generate_constraints function for more info.

generate_constraints(
    ; mono::Vector{Vector{S}}=Vector{String}[],
    not_mono::Vector{Vector{S}}=Vector{String}[],
    exc::Vector{Tuple{Vector{S}, Vector{S}}}=Vector{Tuple{Vector{String}, Vector{String}}}[]
)::ConstraintDict where S<:AbstractString

Generate a dictionary of constraints based on the given arguments. Mono for all monophyletic groups. not_mono for leafs that are not allowed to form a monophletic group. And exc for a partial constraint, where one or more leafs are not allowed to be part of a specific clade.

e.g.: generate_constraints(mono=[["a", "b"], ["a", "c"]], exc=[(["b", "c"],["d"]])

parse_constraints(filename::S
                 )::Tuple{
                    Vector{Vector{S}},
                    Vector{Vector{S}},
                    Vector{Tuple{Vector{S}, Vector{S}}}
                 } where S<:AbstractString

–- INTERNAL –- Helper function that reads constraints out of a file