Advanced Features

Parameter Priors

discoal supports uniform and exponential prior distributions for parameters, useful for ABC and machine learning applications.

Uniform Priors

Most parameters support uniform priors specified with -P flags:

Prior Distribution Flags
Flag	Parameters	Description
`-Pt`	low high	Prior on θ (mutation rate)
`-Pr`	low high	Prior on ρ (recombination rate)
`-Pa`	low high	Prior on α (selection coefficient)
`-Pu`	low high	Prior on τ (time since fixation)
`-PuA`	low high	Prior on uA (recurrent adaptive mutation)
`-Px`	low high	Prior on sweep position
`-Pf`	low high	Prior on f₀ (initial frequency)
`-Pc`	low high	Prior on final sweep frequency

Example:

# Variable mutation and selection parameters
./discoal 20 1000 10000 -Pt 5 50 -Pa 100 2000 -ws 0.01 -x 0.5

Exponential Prior

Recombination rate can follow a truncated exponential:

# Exponential with mean 10, truncated at 100
./discoal 20 100 10000 -t 20 -Pre 10 100

Demographic Priors

Population size changes can have priors:

# Prior on first size change: time 0.01-0.5, size 0.1-10
./discoal 20 100 10000 -t 20 -Pe1 0.01 0.5 0.1 10

# Prior on second size change
./discoal 20 100 10000 -t 20 -Pe1 0.01 0.5 0.1 10 -Pe2 0.5 2.0 0.5 5.0

Conditional Simulations

Simulate conditional on observing recombination in a specific region:

# Condition on recombination between sites 400-600
./discoal 20 100 1000 -t 10 -r 20 -C 400 600

The simulator will retry until this condition is met.

Tree Output Mode

Output genealogical trees in Newick format with -T:

./discoal 10 1 10000 -t 20 -r 10 -T

Output format:

//
[100](0:0.5,1:0.5);
[50]((0:0.2,2:0.2):0.3,1:0.5);
...

Each line shows: [number_of_sites]newick_tree

Recording Recent Mutations

Only record mutations more recent than a specified time:

# Only mutations from last 0.1 time units
./discoal 20 10 10000 -t 50 -U 0.1

Memory and Performance

Large-scale Simulations

For very large simulations:

Increase MAXSITES: Edit discoal.h and recompile
Sample size limit: The maximum sample size is now 65,535 (previously 254)

Performance Tuning

Time discretization: Lower -i values speed up sweeps at potential accuracy cost
Memory efficiency: Current version uses 70-99% less memory than older versions
Parallel runs: Use different random seeds for embarrassingly parallel execution

Setting Random Seeds

For reproducibility:

# Specify both seeds
./discoal 20 10 10000 -t 20 -d 12345 67890

Seeds must be positive integers less than 2^31-1.

Debugging Features

Build with ancestry verification:

make discoal_debug
./discoal_debug 10 1 1000 -t 10 -r 10

This enables additional checks for debugging genealogy construction.