alphabet_cardinality

Julia scripts for the topographical analysis and evolutionary simulations in the paper "Alphabet cardinality and adaptive evolution"

Directory "scripts" contains code to enumerate the number of accessible paths

1. For analysing the RMF landscapes:

julia growing_alpha_RMF.jl type-of-random-adaptive-walk MF-landscape roughness-parameter seed repetition

PARAMETERS:

• type-of-random-adaptive-walk: greedy or equal
• MF-landscape: MF_L=4_$(i).txt ; text file containing Mt. Fuji landscape #i
• roughness parameter: roughness parameter in the RMF model
• seed: specifies the seed of the random number generator
• repetition: specifies repetition number of the alphabet expansion (not the total number of repetitions)

For analysing L=3 RMF landscapes, use script: growing_alpha_RMF_L=3.jl

2. For analysing the ParD-ParE landscapes:

julia growing_alpha_par.jl repetition type-of-random-adaptive-walk landscape

PARAMETERS:

• repetition: specifies repetition number of the alphabet expansion (not the total number of repetitions)
• type-of-random-adaptive-walk: greedy or equal
• landscape: landscape file: map_ParE2.tsv or map_ParE3.tsv

For analysing ParD-ParE landscapes with the number of peaks preserved, use script: growing_alpha_par_samepeaks.jl

3. For analysing the GB1 landscape:

julia growing_alpha_2.jl repetition type-of-random-adaptive-walk landscape

PARAMETERS:

• repetition: specifies repetition number of the alphabet expansion (not the total number of repetitions)
• type-of-random-adaptive-walk: greedy or equal
• landscape: landscape file: map_GB1.tsv