Package | Description |
---|---|
pal.math |
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
|
pal.substmodel |
Classes describing substitution models, i.e.
|
pal.treesearch |
Modifier and Type | Field and Description |
---|---|
static MersenneTwisterFast |
MathUtils.random
A random number generator that is initialized with the clock when this
class is loaded into the JVM.
|
Constructor and Description |
---|
SequenceSimulator(SubstitutionModel model,
int sequenceLength,
MersenneTwisterFast random,
boolean stochasticDistribution)
A constructor (with no provided random number generator - a fresh one is created)
|
Modifier and Type | Method and Description |
---|---|
void |
FreeBranch.doNNI(MersenneTwisterFast r) |
static java.lang.String[][] |
SearcherUtils.split(java.lang.String[] leafNames,
MersenneTwisterFast r) |