Release v0.0.24

Author: holmrenser

CHANGELOG.md

@@ -8,6 +8,15 @@ single version, bumped together via `make bump-{patch,minor,major}`.
 
 ## [Unreleased]
 
+### Added
+- Three substitution models: `TajimaNei` (Tajima-Nei 1984, DNA — corrects
+  Jukes-Cantor for unequal base frequencies), `Tamura` (Tamura 1992, DNA —
+  Kimura two-parameter with a GC-content correction), and `KimuraProtein`
+  (Kimura 1983, protein — empirical correction to the Poisson distance). All are
+  closed-form and reduce to the model they extend under the appropriate
+  conditions (Tajima-Nei → Jukes-Cantor at equal frequencies, Tamura →
+  Kimura-2P at GC = 0.5). Exposed across the CLI, Python, and WASM bindings.
+
 ## [0.0.23] - 2026-06-04
 
 ### Fixed

CLAUDE.md

@@ -89,7 +89,7 @@ FASTA input / SequenceObject list
 
 ### Substitution models (`models.rs`)
 
-Models implement `ModelCalculation<A: AlphabetEncoding>`. DNA-only: `PDiff`, `JukesCantor`, `Kimura2P`. Protein-only: `Poisson`. `PDiff` works for both alphabets. Model–alphabet compatibility is enforced at runtime inside `nj()`.
+Models implement `ModelCalculation<A: AlphabetEncoding>`. DNA-only: `JukesCantor`, `Kimura2P`, `TajimaNei`, `Tamura`. Protein-only: `Poisson`, `KimuraProtein`. `PDiff` works for both alphabets. Model–alphabet compatibility is enforced at runtime inside `nj()` (the `dispatch_run!` macro in `lib.rs`).
 
 ### Bootstrap support
 

Cargo.lock

@@ -7,7 +7,7 @@ opt-level = 3
 lto = true
 
 [workspace.package]
-version = "0.0.23"
+version = "0.0.24"
 edition = "2024"
 authors = ["Rens Holmer"]
 license = "MIT"

Cargo.toml

@@ -46,7 +46,10 @@
 //! | `PDiff` | ✓ | ✓ |
 //! | `JukesCantor` | ✓ | — |
 //! | `Kimura2P` | ✓ | — |
+//! | `TajimaNei` | ✓ | — |
+//! | `Tamura` | ✓ | — |
 //! | `Poisson` | — | ✓ |
+//! | `KimuraProtein` | — | ✓ |
 //!
 //! Providing an incompatible model returns an `Err` from [`nj`].
 pub mod alphabet;
@@ -71,7 +74,9 @@ pub use crate::distance_matrix::DistanceResult;
 pub use crate::error::NJError;
 pub use crate::event::{LogLevel, NJEvent};
 pub use crate::fasta::parse_fasta;
-use crate::models::{JukesCantor, Kimura2P, ModelCalculation, PDiff, Poisson};
+use crate::models::{
+    JukesCantor, Kimura2P, KimuraProtein, ModelCalculation, PDiff, Poisson, TajimaNei, Tamura,
+};
 use crate::tree::{NameOrSupport, TreeNode};
 
 /// Fills `out` with the leaf indices of all taxa in the subtree rooted at `node`.
@@ -553,10 +558,18 @@ macro_rules! dispatch_run {
                     SubstitutionModel::Kimura2P => {
                         $run::<DNA, Kimura2P>(msa, $($arg),*).map_err(NJError::AlgorithmFailure)
                     }
-                    SubstitutionModel::Poisson => Err(NJError::IncompatibleModel {
-                        model,
-                        alphabet: Alphabet::DNA,
-                    }),
+                    SubstitutionModel::TajimaNei => {
+                        $run::<DNA, TajimaNei>(msa, $($arg),*).map_err(NJError::AlgorithmFailure)
+                    }
+                    SubstitutionModel::Tamura => {
+                        $run::<DNA, Tamura>(msa, $($arg),*).map_err(NJError::AlgorithmFailure)
+                    }
+                    SubstitutionModel::Poisson | SubstitutionModel::KimuraProtein => {
+                        Err(NJError::IncompatibleModel {
+                            model,
+                            alphabet: Alphabet::DNA,
+                        })
+                    }
                 }
             }
             Alphabet::Protein => {
@@ -566,15 +579,20 @@ macro_rules! dispatch_run {
                     SubstitutionModel::Poisson => {
                         $run::<Protein, Poisson>(msa, $($arg),*).map_err(NJError::AlgorithmFailure)
                     }
+                    SubstitutionModel::KimuraProtein => {
+                        $run::<Protein, KimuraProtein>(msa, $($arg),*)
+                            .map_err(NJError::AlgorithmFailure)
+                    }
                     SubstitutionModel::PDiff => {
                         $run::<Protein, PDiff>(msa, $($arg),*).map_err(NJError::AlgorithmFailure)
                     }
-                    SubstitutionModel::JukesCantor | SubstitutionModel::Kimura2P => {
-                        Err(NJError::IncompatibleModel {
-                            model,
-                            alphabet: Alphabet::Protein,
-                        })
-                    }
+                    SubstitutionModel::JukesCantor
+                    | SubstitutionModel::Kimura2P
+                    | SubstitutionModel::TajimaNei
+                    | SubstitutionModel::Tamura => Err(NJError::IncompatibleModel {
+                        model,
+                        alphabet: Alphabet::Protein,
+                    }),
                 }
             }
         }