ArticleBioinformatics (Oxford, England)2019
Kalign 3: multiple sequence alignment of large data sets.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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89 citing papers in PubMed.
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- Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.Nature biotechnology · 2026Article
- Rapid and reproducible haplotyping of complete mitochondrial genomes using split k-mers.BMC genomics · 2026Article
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- A novel COE-D8-fosfomycin conjugate effectively combats first-line antibiotic-resistant uropathogenic Escherichia coli.PloS one · 2026Article
- Spatiotemporal dynamics of benthicFrontiers in microbiology · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- A transcription factor gene CaMYB114 associated with black seed coat in chickpea.BMC plant biology · 2025Article
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29 more citing papers are in PubMed but not listed here.
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Authors and funding
1 author.
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No grant is acknowledged in the PubMed record.
Abstract
motivationKalign is an efficient multiple sequence alignment (MSA) program capable of aligning thousands of protein or nucleotide sequences. However, current alignment problems involving large numbers of sequences are exceeding Kalign's original design specifications. Here we present a completely re-written and updated version to meet current and future alignment challenges.
resultsKalign now uses a SIMD accelerated version of the bit-parallel Gene Myers algorithm to estimate pariwise distances, adopts a sequence embedding strategy and the bi-secting K-means algorithm to rapidly construct guide trees for thousands of sequences. The new version maintains high alignment accuracy on both protein and nucleotide alignments and scales better than other MSA tools. AVAILABILITY: The source code of Kalign and code to reproduce the results are found here: https://github.com/timolassmann/kalign.
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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.