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.
☆276Apr 2, 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:
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆255Apr 1, 2026Updated last week
- Align multiple amino acid or nucleotide sequences.☆79Sep 17, 2020Updated 5 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- A fast multiple sequence alignment program.☆154Apr 1, 2026Updated last week
- Manipulate and generate figures for trees in Newick format☆22Jul 31, 2025Updated 8 months ago
- 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.
- Accelerated BLAST compatible local sequence aligner.☆1,278Mar 28, 2026Updated last week
- Simple pileup-based variant caller☆95Apr 25, 2025Updated 11 months ago
- Mummer alignment tool☆554Feb 4, 2025Updated last year
- HMMER: biological sequence analysis using profile HMMs☆407Feb 16, 2026Updated last month
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,536Mar 31, 2026Updated last week
- Version 5 of the CAFE phylogenetics software☆164Mar 16, 2026Updated 3 weeks ago
- Synteny and Rearrangement Identifier☆458Mar 17, 2026Updated 3 weeks ago
- Constructing a pangenome gene graph☆205Aug 11, 2025Updated 7 months ago
- A genome completeness evaluation tool based on miniprot☆237Sep 18, 2025Updated 6 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- IQ-TREE version 3: software for phylogenetics☆121Apr 2, 2026Updated last week
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆190Jan 29, 2026Updated 2 months ago
- Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)☆225Mar 23, 2026Updated 2 weeks ago
- Align proteins to genomes with splicing and frameshift☆397Jan 5, 2026Updated 3 months ago
- Chromosome-level scaffolding using multiple references☆165Sep 8, 2024Updated last year
- Long read aligner☆114May 26, 2023Updated 2 years ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆160Apr 1, 2026Updated last week
- Automatically exported from code.google.com/p/cdhit☆723Oct 11, 2022Updated 3 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 7 months ago
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- Visualizing publication-quality multiple sequence alignment using ggplot2☆217Nov 1, 2025Updated 5 months ago
- MMseqs2: ultra fast and sensitive search and clustering suite☆2,015Updated this week
- Tool to plot synteny and structural rearrangements between genomes☆344Apr 7, 2025Updated last year
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Sep 2, 2025Updated 7 months ago
- SPAdes Genome Assembler☆921Mar 17, 2026Updated 3 weeks ago
- Protein structure alignment and search algorithm☆80Updated this week
- Extensive de-novo TE Annotator☆438Updated this week
- linearize and simplify variation graphs using blocked partial order alignment☆62Mar 31, 2026Updated last week
- Tandem Repeats Finder: a program to analyze DNA sequences☆204Jan 16, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A tool for generating consensus long-read assemblies for bacterial genomes☆341Sep 11, 2025Updated 6 months ago
- A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence☆112Oct 2, 2025Updated 6 months ago
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆325Mar 12, 2026Updated 3 weeks ago
- Fast Whole-Genome Similarity (ANI) Estimation☆452Dec 16, 2025Updated 3 months ago
- geNomad: Identification of mobile genetic elements☆297Mar 29, 2026Updated last week
- Official home of genome aligner based upon notion of Cactus graphs☆669Updated this week
- De novo genome assembler for long uncorrected reads☆231Nov 15, 2023Updated 2 years ago