Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
☆256Apr 15, 2026Updated 2 months ago
Alternatives and similar repositories for FAMSA
Users that are interested in FAMSA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.☆44Mar 24, 2026Updated 3 months ago
- ☆135Aug 29, 2024Updated last year
- sensitive and precise assembly of short sequencing reads☆167Oct 11, 2024Updated last year
- MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics☆207Aug 25, 2025Updated 10 months ago
- MMseqs2: ultra fast and sensitive search and clustering suite☆2,090Jun 21, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A fast multiple sequence alignment program.☆160Jun 20, 2026Updated last week
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 4 years ago
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆109May 23, 2025Updated last year
- Align proteins to genomes with splicing and frameshift☆405Jan 5, 2026Updated 5 months ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆77Jun 17, 2024Updated 2 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆263Updated this week
- Genome mapping and spliced alignment of cDNA or amino acid sequences☆113Feb 28, 2026Updated 4 months ago
- ☆19May 10, 2023Updated 3 years ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆312Feb 3, 2026Updated 4 months ago
- 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.
- Efficient phylogenetic tree inference for massive taxonomic datasets☆145Apr 6, 2025Updated last year
- ☆16Jan 28, 2026Updated 5 months ago
- Aligns short reads using dynamic seed size with strobemers☆202Updated this week
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆216Apr 24, 2026Updated 2 months ago
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆179Apr 6, 2026Updated 2 months ago
- Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.☆90Mar 27, 2026Updated 3 months ago
- Cython bindings and Python interface to HMMER3.☆165May 27, 2026Updated last month
- Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins☆183Jun 11, 2026Updated 2 weeks ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated 2 years ago
- 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.
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆60Jan 7, 2026Updated 5 months ago
- Multiple Protein Structure Alignment at Scale with FoldMason☆281May 11, 2026Updated last month
- Remote protein homology detection suite.☆622Aug 12, 2025Updated 10 months ago
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆101May 14, 2026Updated last month
- Bacterial Annotation by Learned Representation of Genes☆60Mar 26, 2026Updated 3 months ago
- Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshift☆19Sep 30, 2024Updated last year
- WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.☆13Nov 18, 2025Updated 7 months ago
- A package to annotate protein sequences☆63Feb 23, 2025Updated last year
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆189Mar 17, 2026Updated 3 months ago
- 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.
- Compressing protein structures effectively with torsion angles☆193Feb 10, 2026Updated 4 months ago
- geNomad: Identification of mobile genetic elements☆318Mar 29, 2026Updated 3 months ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆217Jun 21, 2026Updated last week
- Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, e…☆284Apr 20, 2026Updated 2 months ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated 11 months ago
- A grammar of graphics for comparative genomics☆768Feb 23, 2026Updated 4 months ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago