Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
☆288Apr 20, 2026Updated 3 months ago
Alternatives and similar repositories for muscle
Users that are interested in muscle are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Align multiple amino acid or nucleotide sequences.☆95Sep 17, 2020Updated 5 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆268Updated this week
- Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)☆270Jul 20, 2026Updated 3 weeks ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆27Apr 29, 2024Updated 2 years ago
- A fast multiple sequence alignment program.☆162Jul 22, 2026Updated 2 weeks ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Manipulate and generate figures for trees in Newick format☆22Jul 31, 2025Updated last year
- Simple pileup-based variant caller☆96Apr 25, 2025Updated last year
- Accelerated BLAST compatible local sequence aligner.☆1,313Aug 4, 2026Updated last week
- Mummer alignment tool☆571Feb 4, 2025Updated last year
- HMMER: biological sequence analysis using profile HMMs☆418Jul 14, 2026Updated 3 weeks ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,589Jul 8, 2026Updated last month
- Version 5 of the CAFE phylogenetics software☆176Mar 16, 2026Updated 4 months ago
- Synteny and Rearrangement Identifier☆482Jul 1, 2026Updated last month
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆173Aug 1, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A genome completeness evaluation tool based on miniprot☆259Jul 29, 2026Updated last week
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆202Jan 29, 2026Updated 6 months ago
- Constructing a pangenome gene graph☆210Aug 11, 2025Updated last year
- Open-source usearch☆142May 24, 2026Updated 2 months ago
- Align proteins to genomes with splicing and frameshift☆414Jan 5, 2026Updated 7 months ago
- Chromosome-level scaffolding using multiple references☆170Sep 8, 2024Updated last year
- Long read aligner☆115May 26, 2023Updated 3 years ago
- Automatically exported from code.google.com/p/cdhit☆732Oct 11, 2022Updated 3 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆145Aug 24, 2025Updated 11 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Tool to plot synteny and structural rearrangements between genomes☆351Jul 27, 2026Updated 2 weeks ago
- Visualizing publication-quality multiple sequence alignment using ggplot2☆219Jun 9, 2026Updated 2 months ago
- MMseqs2: ultra fast and sensitive search and clustering suite☆2,124Jul 25, 2026Updated 2 weeks ago
- SPAdes Genome Assembler☆956Jun 16, 2026Updated last month
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Apr 20, 2026Updated 3 months ago
- Protein structure alignment and search algorithm☆98Jul 31, 2026Updated last week
- Extensive de-novo TE Annotator☆466Jul 16, 2026Updated 3 weeks ago
- Tandem Repeats Finder: a program to analyze DNA sequences☆216Jan 16, 2023Updated 3 years ago
- linearize and simplify variation graphs using blocked partial order alignment☆63Jul 27, 2026Updated 2 weeks ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A tool for generating consensus long-read assemblies for bacterial genomes☆347Jul 24, 2026Updated 2 weeks ago
- A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence☆116Jul 21, 2026Updated 2 weeks ago
- Official home of genome aligner based upon notion of Cactus graphs☆700Updated this week
- Fast Whole-Genome Similarity (ANI) Estimation☆477Dec 16, 2025Updated 7 months ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆91Mar 12, 2026Updated 4 months ago
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆335Jul 22, 2026Updated 2 weeks ago
- De novo genome assembler for long uncorrected reads☆232Nov 15, 2023Updated 2 years ago