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mafft_core/
lib.rs

1//! Core MAFFT alignment engine.
2//!
3//! Orchestrates the full alignment pipeline:
4//! 1. Progressive alignment following a guide tree.
5//! 2. Iterative refinement with score-based acceptance.
6//! 3. Adding sequences to existing alignments.
7//!
8//! Ports the C `TreeDependentIteration()` from `tditeration.c`,
9//! progressive alignment from `disttbfast.c`/`tbfast.c`, and
10//! `addonetip()` from `addfunctions.c`.
11
12pub mod adjust_direction;
13pub mod progressive;
14mod varidist;
15mod refinement;
16mod engine;
17mod add;
18pub mod external;
19
20pub use progressive::{progressive_align, progressive_align_partial, progressive_align_unweighted, progressive_align_with_weights_override, MultipleAlignment, StepTrace};
21pub use refinement::{iterative_refine, RefinementParams};
22pub use engine::{MafftEngine, AlignmentMode, pair_penalty_scales, dndpre_offset_shift};
23pub use add::{add_sequences, add_sequences_keeplength, add_sequences_keeplength_with_map};