Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
☆270Jul 20, 2026Updated last month
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.☆46Mar 24, 2026Updated 5 months ago
- Discovery of conserved gene clusters in multiple genomes☆135Aug 21, 2026Updated last week
- Align proteins to genomes with splicing and frameshift☆417Jan 5, 2026Updated 7 months ago
- sensitive and precise assembly of short sequencing reads☆169Oct 11, 2024Updated last year
- ☆137Aug 29, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆316Feb 3, 2026Updated 6 months ago
- MMseqs2: ultra fast and sensitive search and clustering suite☆2,132Updated this week
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆226Aug 22, 2026Updated last week
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆182Jul 22, 2026Updated last month
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆269Updated this week
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆110Jul 7, 2026Updated last month
- MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics☆210Aug 25, 2025Updated last year
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆77Jun 17, 2024Updated 2 years ago
- Multiple Protein Structure Alignment at Scale with FoldMason☆281May 11, 2026Updated 3 months ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆190Mar 17, 2026Updated 5 months ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆63Jul 5, 2026Updated last month
- A fast multiple sequence alignment program.☆162Jul 22, 2026Updated last month
- Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, e…☆289Updated this week
- Aligns short reads using dynamic seed size with strobemers☆203Updated this week
- FastOMA is a scalable software package to infer orthology relationship.☆102Updated this week
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆102Updated this week
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 4 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆222Updated this week
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Fast indexing and search of discontinuous motifs in protein structures☆213Jul 10, 2026Updated last month
- Genome mapping and spliced alignment of cDNA or amino acid sequences☆114Jul 11, 2026Updated last month
- Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!☆27Mar 25, 2026Updated 5 months ago
- Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly☆229Jul 22, 2026Updated last month
- A grammar of graphics for comparative genomics☆779Updated this week
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆670Aug 7, 2026Updated 3 weeks ago
- Cython bindings and Python interface to HMMER3.☆169Aug 19, 2026Updated last week
- Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads☆53Aug 17, 2026Updated last week
- A new high-resolution long-read metagenome assembler for even noisy reads☆166Jul 3, 2026Updated last month
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Efficient phylogenetic tree inference for massive taxonomic datasets☆147Apr 6, 2025Updated last year
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆263May 13, 2026Updated 3 months ago
- Phage Annotation using Protein Structures☆171Updated this week
- Gene cluster comparison figure generator☆652Dec 22, 2025Updated 8 months ago
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆229May 9, 2026Updated 3 months ago
- A package to annotate protein sequences☆63Feb 23, 2025Updated last year
- geNomad: Identification of mobile genetic elements☆328Mar 29, 2026Updated 5 months ago