Crate nj 

Neighbor-Joining phylogenetic tree inference library.

Data flow

[FASTA / Python dict / JS object]
        │
        ▼
     NJConfig  (config.rs)
        │
        ▼
  detect_alphabet()  ──►  Alphabet::DNA | Alphabet::Protein
        │
        ▼
    MSA<DNA|Protein>  (msa.rs)
     ├── bootstrap() ──► bootstrap_clade_counts()
     └── into_dist::<Model>()
              │
              ▼
          DistMat  (dist.rs)
              │
              ▼
        neighbor_joining()  ──►  NJState::run()  (nj.rs)
              │
              ▼
          TreeNode  (tree.rs)
              │
              ▼
          to_newick()  ──►  Newick String

Public API

The single public entry point is [nj], which accepts an NJConfig and returns a Newick string. Everything else is internal implementation detail exposed only to the Python and WASM wrapper crates.

Model–alphabet compatibility

Model	DNA	Protein
PDiff	✓	✓
JukesCantor	✓	—
Kimura2P	✓	—
Poisson	—	✓

Providing an incompatible model returns an Err from [nj].

Re-exports

pub use crate::config::DistConfig;

pub use crate::config::MSA;

pub use crate::config::NJConfig;

pub use crate::config::NJResult;

pub use crate::config::SequenceObject;

pub use crate::distance_matrix::DistanceResult;

pub use crate::error::NJError;

pub use crate::event::LogLevel;

pub use crate::event::NJEvent;

pub use crate::fasta::parse_fasta;

Modules

alphabet

Alphabet definitions and encoding for DNA and protein sequences.

config

Public configuration types shared between the core library, Python bindings, and WASM bindings.

distance_matrix

Lower-triangular pairwise distance matrix and entry point for NJ.

error

Error type for the nj library.

event

Event types fired by the NJ algorithm and forwarded to wrapper callbacks.

fasta

FASTA parser for multiple sequence alignment input.

models

Substitution models for computing pairwise evolutionary distances.

msa

Multiple sequence alignment container and bootstrap resampling.

nj

Core Neighbor-Joining algorithm implementation.

tree

Binary tree representation for Neighbor-Joining output.

Functions

average_distance

Computes the mean of all n*(n-1)/2 unique pairwise distances.

distance_matrix

Computes pairwise distances from an aligned MSA and returns a DistanceResult.

nj

Infers a phylogenetic tree from an aligned MSA and returns an NJResult.