Rivet

A fast, modern implementation of the STAMP (Structural Alignment of Multiple Proteins) algorithm in Rust with Python bindings.

Features

Full PDB Output: Aligns and transforms complete structures (all atoms), not just C-alpha
Simple API: One function call to align multiple PDB files and write output
Fast: Written in Rust for maximum performance
Safe: Memory-safe by design, zero unsafe code
Cross-platform: Linux, macOS, and Windows

Installation

pip install rivet-rs

Quick Start

Align Multiple Structures (Simplest)

import rivet

# Align PDB files and write full structures to output directory
result = rivet.align_pdbs(
    ["protein1.pdb", "protein2.pdb", "protein3.pdb"],
    output_dir="aligned/",
    chain="A"
)

print(f"Average RMSD: {result.avg_rmsd:.2f} Å")
print(f"Core positions: {result.n_core}")
# Output files written to aligned/aligned_protein1.pdb, etc.

Pairwise Alignment

import rivet

# Load structures
d1 = rivet.Domain.from_pdb("reference.pdb", chain="A")
d2 = rivet.Domain.from_pdb("mobile.pdb", chain="A")

# Align (use scan_mode=True for structures in different coordinate frames)
result = rivet.pairwise_align(d1, d2, scan_mode=True)

print(f"RMSD: {result.rmsd:.2f} Å")
print(f"Score: {result.score:.4f}")
print(f"Aligned: {result.n_aligned} residues")

# Write aligned structure (full PDB with all atoms by default)
d2.to_pdb("mobile_aligned.pdb", transform=result.transform)

Parameters for Remote Homologs

When comparing distantly related structures, use tolerant parameters:

params = rivet.Parameters()
params.e1 = 5.0   # Distance tolerance (default: 2.0)
params.e2 = 10.0  # Conformational tolerance (default: 5.0)

result = rivet.pairwise_align(d1, d2, params, scan_mode=True)

Output Options

By default, to_pdb() writes the full structure (all atoms: backbone, side chains, waters, ligands):

# Default: full structure with all atoms
d2.to_pdb("output.pdb", transform=result.transform)

# Explicit: C-alpha only (smaller file, faster)
d2.to_pdb("output_ca.pdb", transform=result.transform, full=False)

Multiple Alignment with Manual Control

For more control over the alignment process:

import rivet

# Load domains
domains = [
    rivet.Domain.from_pdb("protein1.pdb", chain="A"),
    rivet.Domain.from_pdb("protein2.pdb", chain="A"),
    rivet.Domain.from_pdb("protein3.pdb", chain="A"),
]

params = rivet.Parameters()
params.e1 = 5.0
params.e2 = 10.0

# Step 1: Pre-align to reference
aligned_domains = [domains[0]]
pre_transforms = [rivet.Transform()]

for i in range(1, len(domains)):
    result = rivet.pairwise_align(domains[0], domains[i], params, scan_mode=True)
    pre_transforms.append(result.transform)

    # Create pre-aligned domain
    coords = result.get_transformed_coordinates(domains[i])
    aligned = rivet.Domain.from_arrays(
        domains[i].id, coords, domains[i].sequence, chain=domains[i].chain
    )
    aligned_domains.append(aligned)

# Step 2: Run multiple alignment
result = rivet.multiple_align(aligned_domains, params, pre_transforms=pre_transforms)

# Step 3: Write output using composed transforms
original_files = ["protein1.pdb", "protein2.pdb", "protein3.pdb"]
for pdb_file, full_transform in zip(original_files, result.full_transforms):
    rivet.transform_pdb_file(pdb_file, f"aligned_{pdb_file}", full_transform)

Database Scanning

query = rivet.Domain.from_pdb("query.pdb", chain="A")
targets = [rivet.Domain.from_pdb(f, chain="A") for f in target_files]

hits = rivet.scan_database(query, targets, score_cutoff=0.3)

for hit in hits:
    print(f"{hit.target_id}: Score={hit.score:.4f}, RMSD={hit.rmsd:.2f} Å")

Rust API

Add to your Cargo.toml:

[dependencies]
stamp-core = "0.1"

use stamp_core::{io::{parse_pdb, transform_pdb}, pairwise::align_pair, types::Parameters};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let d1 = parse_pdb("reference.pdb", Some('A'))?;
    let d2 = parse_pdb("mobile.pdb", Some('A'))?;

    let params = Parameters::default();
    let result = align_pair(&d1, &d2, &params)?;

    println!("RMSD: {:.2} Å, Score: {:.4}", result.rmsd, result.score);

    // Transform full PDB (all atoms)
    transform_pdb("mobile.pdb", "mobile_aligned.pdb", &result.transform, None)?;

    Ok(())
}

API Reference

Functions

Function	Description
`align_pdbs(files, output_dir, ...)`	High-level: align PDB files and write output
`pairwise_align(d1, d2, params, scan_mode)`	Align two structures
`multiple_align(domains, params, pre_transforms)`	Multiple structure alignment
`transform_pdb_file(input, output, transform)`	Transform full PDB file
`scan_database(query, targets, ...)`	Scan query against database
`compute_rmsd(coords1, coords2)`	Compute RMSD
`superpose(fixed, mobile)`	Optimal superposition

Classes

Class	Description
`Domain`	Protein domain with coordinates
`Parameters`	Alignment parameters
`Transform`	3D rigid body transformation
`AlignmentResult`	Pairwise alignment result
`MultipleAlignmentResult`	Multiple alignment result with `full_transforms`

Key Parameters

Parameter	Default	Description
`e1`	2.0	Distance tolerance (Å) - increase for remote homologs
`e2`	5.0	Conformational tolerance (Å) - increase for flexible regions
`n_passes`	2	Number of refinement passes
`scan_mode`	False	Enable sliding window scan for different coordinate frames

Algorithm

STAMP uses the Rossmann-Argos probability measure for structural equivalence:

Calculate probability matrix based on inter-residue distances
Smith-Waterman dynamic programming to find optimal alignment
Extract equivalent residue pairs above threshold
Compute optimal superposition (Kabsch algorithm)
Iterate until convergence

References:

Russell & Barton, Proteins 14:309-323 (1992)
Rossmann & Argos, J. Mol. Biol. 105:75-95 (1976)

License

MIT License - see LICENSE for details.

Citation

@article{russell1992multiple,
  title={Multiple protein sequence alignment from tertiary structure comparison},
  author={Russell, Robert B and Barton, Geoffrey J},
  journal={Proteins: Structure, Function, and Bioinformatics},
  volume={14},
  number={2},
  pages={309--323},
  year={1992}
}

Release files for rivet-rs 0.1.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Built distributions (wheels)

Table of built distributions (wheels) for rivet-rs 0.1.2
File	Interpreter	ABI	Platform	Reset
rivet_rs-0.1.2-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 387.5 kB Jan 14, 2026	PyPy 3.11	PyPy 3.11 7.3	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-pp311-pypy311_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 369.8 kB Jan 14, 2026	PyPy 3.11	PyPy 3.11 7.3	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp314-cp314t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 369.5 kB Jan 14, 2026	CPython 3.14	CPython 3.14 free-threading	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp314-cp314-win_amd64.whl 296.7 kB Jan 14, 2026	CPython 3.14	CPython 3.14	Windows x86-64	Details
rivet_rs-0.1.2-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 390.8 kB Jan 14, 2026	CPython 3.14	CPython 3.14	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-cp314-cp314-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 372.4 kB Jan 14, 2026	CPython 3.14	CPython 3.14	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp314-cp314-macosx_11_0_arm64.whl 352.2 kB Jan 14, 2026	CPython 3.14	CPython 3.14	macOS 11.0+ ARM64	Details
rivet_rs-0.1.2-cp314-cp314-macosx_10_12_x86_64.whl 376.9 kB Jan 14, 2026	CPython 3.14	CPython 3.14	macOS 10.12+ x86-64	Details
rivet_rs-0.1.2-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 371.7 kB Jan 14, 2026	CPython 3.13	CPython 3.13 free-threading	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp313-cp313-win_amd64.whl 294.2 kB Jan 14, 2026	CPython 3.13	CPython 3.13	Windows x86-64	Details
rivet_rs-0.1.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 388.9 kB Jan 14, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 370.5 kB Jan 14, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp313-cp313-macosx_11_0_arm64.whl 349.8 kB Jan 14, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ ARM64	Details
rivet_rs-0.1.2-cp313-cp313-macosx_10_12_x86_64.whl 374.8 kB Jan 14, 2026	CPython 3.13	CPython 3.13	macOS 10.12+ x86-64	Details
rivet_rs-0.1.2-cp312-cp312-win_amd64.whl 294.3 kB Jan 14, 2026	CPython 3.12	CPython 3.12	Windows x86-64	Details
rivet_rs-0.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 389.1 kB Jan 14, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 370.7 kB Jan 14, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp312-cp312-macosx_11_0_arm64.whl 350.3 kB Jan 14, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ ARM64	Details
rivet_rs-0.1.2-cp312-cp312-macosx_10_12_x86_64.whl 375.1 kB Jan 14, 2026	CPython 3.12	CPython 3.12	macOS 10.12+ x86-64	Details
rivet_rs-0.1.2-cp311-cp311-win_amd64.whl 293.4 kB Jan 14, 2026	CPython 3.11	CPython 3.11	Windows x86-64	Details
rivet_rs-0.1.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 387.0 kB Jan 14, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 369.6 kB Jan 14, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp311-cp311-macosx_11_0_arm64.whl 351.3 kB Jan 14, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ ARM64	Details
rivet_rs-0.1.2-cp311-cp311-macosx_10_12_x86_64.whl 374.9 kB Jan 14, 2026	CPython 3.11	CPython 3.11	macOS 10.12+ x86-64	Details
rivet_rs-0.1.2-cp310-cp310-win_amd64.whl 293.2 kB Jan 14, 2026	CPython 3.10	CPython 3.10	Windows x86-64	Details
rivet_rs-0.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 387.1 kB Jan 14, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 369.7 kB Jan 14, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.17+ ARM64	Details
rivet_rs-0.1.2-cp39-cp39-win_amd64.whl 294.2 kB Jan 14, 2026	CPython 3.9	CPython 3.9	Windows x86-64	Details
rivet_rs-0.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 388.2 kB Jan 14, 2026	CPython 3.9	CPython 3.9	Linux glibc 2.17+ x86-64	Details
rivet_rs-0.1.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 370.7 kB Jan 14, 2026	CPython 3.9	CPython 3.9	Linux glibc 2.17+ ARM64	Details

Total release size: 10.7 MB

Release files / rivet_rs-0.1.2-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL	rivet_rs-0.1.2-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Publishing logs: github.com/msinclair-py/rivet/actions/runs/21013231542/attempts/1

Artifact

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Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp313-cp313-macosx_11_0_arm64.whl

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Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp313-cp313-macosx_10_12_x86_64.whl

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Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp312-cp312-win_amd64.whl

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Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Provenance

Identity

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Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp312-cp312-macosx_11_0_arm64.whl

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp312-cp312-macosx_10_12_x86_64.whl

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp311-cp311-win_amd64.whl

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Provenance

Identity

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Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Upload date	Jan 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.7`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp311-cp311-macosx_11_0_arm64.whl

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Release files / rivet_rs-0.1.2-cp311-cp311-macosx_10_12_x86_64.whl

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Release files / rivet_rs-0.1.2-cp310-cp310-win_amd64.whl

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Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Release files / rivet_rs-0.1.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Release files / rivet_rs-0.1.2-cp39-cp39-win_amd64.whl

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Uploaded via	`twine/6.1.0 CPython/3.13.7`

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Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Uploaded via	`twine/6.1.0 CPython/3.13.7`

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Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release files / rivet_rs-0.1.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

Download URL	rivet_rs-0.1.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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Uploaded via	`twine/6.1.0 CPython/3.13.7`

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Publishing platform: GitHub Actions
Publishing repository: github.com/msinclair-py/rivet
Publishing commit: github.com/msinclair-py/rivet/tree/1ae9bdddb1e95e97ea5254f418edd2f42ca75c21

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Release history Release notifications | RSS feed

This release

0.1.2 This release

Jan 14, 2026 30 release files

0.1.1

Jan 14, 2026 30 release files

0.1.0

Jan 14, 2026 29 release files

rivet-rs 0.1.2

Rivet

Features

Installation

Quick Start

Align Multiple Structures (Simplest)

Pairwise Alignment

Parameters for Remote Homologs

Output Options

Multiple Alignment with Manual Control

Database Scanning

Rust API

API Reference

Functions

Classes

Key Parameters

Algorithm

License

Citation

Project links

Key dates

1 maintainer

Credits

License expression

Requires

Provides Extra

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Release files for rivet-rs 0.1.2

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