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.
☆289Aug 24, 2026Updated last week
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.☆96Sep 17, 2020Updated 5 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆269Updated this week
- Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)☆270Jul 20, 2026Updated last month
- 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 last month
- 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.☆1,316Aug 4, 2026Updated 3 weeks ago
- Mummer alignment tool☆573Feb 4, 2025Updated last year
- HMMER: biological sequence analysis using profile HMMs☆419Jul 14, 2026Updated last month
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,590Aug 21, 2026Updated last week
- Version 5 of the CAFE phylogenetics software☆177Mar 16, 2026Updated 5 months ago
- Synteny and Rearrangement Identifier☆485Jul 1, 2026Updated last month
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆174Aug 19, 2026Updated last week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A genome completeness evaluation tool based on miniprot☆262Aug 17, 2026Updated last week
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆203Jan 29, 2026Updated 7 months ago
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year
- Open-source usearch☆142Aug 19, 2026Updated last week
- Align proteins to genomes with splicing and frameshift☆417Jan 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☆731Oct 11, 2022Updated 3 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆145Aug 24, 2025Updated last year
- 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☆354Jul 27, 2026Updated last month
- Visualizing publication-quality multiple sequence alignment using ggplot2☆220Jun 9, 2026Updated 2 months ago
- MMseqs2: ultra fast and sensitive search and clustering suite☆2,132Aug 24, 2026Updated last week
- SPAdes Genome Assembler☆956Jun 16, 2026Updated 2 months ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Apr 20, 2026Updated 4 months ago
- Protein structure alignment and search algorithm☆99Updated this week
- Extensive de-novo TE Annotator☆469Jul 16, 2026Updated last month
- 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☆64Aug 21, 2026Updated last week
- 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☆348Jul 24, 2026Updated last month
- A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence☆117Jul 21, 2026Updated last month
- Official home of genome aligner based upon notion of Cactus graphs☆703Updated this week
- Fast Whole-Genome Similarity (ANI) Estimation☆479Dec 16, 2025Updated 8 months ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆91Mar 12, 2026Updated 5 months ago
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆335Jul 22, 2026Updated last month
- De novo genome assembler for long uncorrected reads☆233Nov 15, 2023Updated 2 years ago