ArticleScientific reports2016
FAMSA: Fast and accurate multiple sequence alignment of huge protein families.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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Who cites it
122 citing papers in PubMed.
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- Eukaryotic-like microtubules and dynamic instability of Asgard archaeal tubulins.Science advances · 2026Article
- Ec_Ou_ZC1, a new Tunavirus, reveals Cor superinfection exclusion and differential Avs susceptibility across Drexlerviridae subfamilies.BMC microbiology · 2026Article
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- Contrasting evolutionary patterns of helper and sensor NRC NLRs in lettuce reflect functional divergence following subfunctionalization.PLoS genetics · 2026Article
- Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes.The Plant journal : for cell and molecular biology · 2026Article
- A lipid cue drives the subcellular localization of a self-inserting bacterial transmembrane protein.bioRxiv : the preprint server for biology · 2026Article
- Early hexapod genomes reveal the deep origin of insect gustatory and odorant receptors.Nature communications · 2026Article
- The heterogeneous selection landscape of genome evolution in prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.Protein science : a publication of the Protein Society · 2026Article
- Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.Nature biotechnology · 2026Article
- Article
- Deep-branching Chloroflexota lineages illuminate the eco-evolutionary foundation of cross-ecosystem colonization.Nature communications · 2026Article
- Exploiting evolutionary diversity of cellulose synthase catalytic subunits to generate novel cellulose microfibril structure in Arabidopsis.Journal of experimental botany · 2026Article
- Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling.Nature microbiology · 2026Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms, such as Clustal Omega or MAFFT for datasets exceeding a few thousand sequences. Quality does not compromise on time or memory requirements, which are an order of magnitude lower than those in the existing solutions. For example, a family of 415519 sequences was analyzed in less than two hours and required no more than 8 GB of RAM. FAMSA is available for free at http://sun.aei.polsl.pl/REFRESH/famsa.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.