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.

Modules

models

Structs

MSA

A typed multiple sequence alignment (MSA).

NJConfig

Full configuration for a single Neighbor-Joining run.

SequenceObject

A single sequence in a multiple sequence alignment.

Functions

bootstrap_clade_counts

Performs bootstrap sampling and counts clades across bootstrap trees.

count_clades

Recursively counts how many times each non-trivial clade appears in tree.

detect_alphabet

Heuristically detects whether the MSA contains DNA or protein sequences.

nj

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