ArticleBioinformatics (Oxford, England)2019
VIRULIGN: fast codon-correct alignment and annotation of viral genomes.
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 40 papers, 1 of them a synthesis that pooled it.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.Viruses · 2025Pooled it
- Men who have sex with men newly diagnosed with HIV-1 in Portugal (2023-2024): a comparative analysis of transmission clusters between migrants and non-migrants.Scientific reports · 2026Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Sources of Human Immunodeficiency Virus Infections Among Men Who Have Sex With Men With a Migration Background: A Viral Phylogenetic Case Study in Amsterdam, The Netherlands.The Journal of infectious diseases · 2024Article
- MARVEL-minimising the emergence and dissemination of HIV-1 drug resistance in Portuguese-speaking African Countries (PALOP): low-cost portable NGS platform for HIV-1 surveillance in Africa.BMC infectious diseases · 2024Article
- HIV-1 diversity and pre-treatment drug resistance in the era of integrase inhibitor among newly diagnosed ART-naïve adult patients in Luanda, Angola.Scientific reports · 2024Article
- UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example.BMC genomics · 2024Article
- Applying Next-Generation Sequencing to Track HIV-1 Drug Resistance Mutations Circulating in Portugal.Viruses · 2024Article
- CNCA aligns small annotated genomes.BMC bioinformatics · 2024Article
- Article
- Evolutionary trajectory of SARS-CoV-2 genome shifts during widespread vaccination and emergence of Omicron variant.Npj viruses · 2023Article
- Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding.Bioinformatics (Oxford, England) · 2023Article
- Use of whole genome sequencing to identify low-frequency mutations in SARS-CoV-2 patients treated with remdesivir.Influenza and other respiratory viruses · 2023Article
- COVID Variants, Villain and Victory: A Bioinformatics Perspective.Microorganisms · 2023Article
- Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the U.S. Using Phylogeography.Pathogens (Basel, Switzerland) · 2023Article
- Genetic Characterization of a NovelViruses · 2023Article
- Investigation of the individual genetic evolution of SARS-CoV-2 in a small cluster during the rapid spread of the BF.5 lineage in Tokyo, Japan.Frontiers in microbiology · 2023Article
- Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.Nature microbiology · 2022Article
- Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam.eLife · 2022Article
- Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design.Genes & genomics · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryVirus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. AVAILABILITY AND IMPLEMENTATION: VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.
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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.