Expand description
Substitution models for computing pairwise evolutionary distances.
All models implement ModelCalculation via a three-phase accumulator
pattern over aligned column pairs: init → per-column
accumulate → finalize.
Gap positions are skipped during accumulation, but the full alignment length
is always used as the denominator in the final distance formula.
Structs§
- Jukes
Cantor - Jukes-Cantor (1969) distance for DNA.
- Kimura2P
- Kimura two-parameter (1980) distance for DNA.
- PDiff
- p-distance (proportion of differing sites).
- Poisson
- Poisson distance for protein sequences.
Enums§
- Substitution
Model - Available substitution models.
Traits§
- Model
Calculation - Trait for substitution model calculations over a given alphabet.
Functions§
- pairwise_
distance - Computes the pairwise distance between two aligned sequences using model
M.