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::MSA;

pub use crate::config::NJConfig;

pub use crate::config::SequenceObject;

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.

models

msa

Multiple sequence alignment container and bootstrap resampling.

nj

Core Neighbor-Joining algorithm implementation.

tree

Binary tree representation for Neighbor-Joining output.

Functions

nj

Infers a phylogenetic tree from an aligned MSA and returns a Newick string.