Additional tools connected to/embedded within INSaFLU-TELEVIR
Tools connected to / embedded within INSaFLU-TELEVIR
- Pangolin - developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as Pango nomenclature
- Code - https://github.com/cov-lineages/pangolin
- Website - https://cov-lineages.org/resources/pangolin.html
- Publications - O'Toole, Á., et al. Vírus Evolution. (2021) (https://doi.org/10.1093/ve/veab064) and Rambaut, A., Holmes, E.C., et al. Nature Microbiology. (2020) (https://doi.org/10.1038/s41564-020-0770-5)
- Nextstrain - from consensus sequences to phylogeographic and temporal analysis and metadatada navigation
- Code - https://github.com/nextstrain
- Website - https://nextstrain.org/
- Publication - Hadfield, J., et al. Bioinformatics. (2018) (https://doi.org/10.1093/bioinformatics/bty407)
- Nextclade - performs genetic sequence alignment, clade assignment, mutation calling, phylogenetic placement, and quality checks for various pathogens.
- Web tool - https://clades.nextstrain.org/
- Code - https://github.com/nextstrain/nextclade
- algn2pheno - a bioinformatics tool for rapid screening of genetic features (nt or aa changes) potentially linked to specific phenotypes
- Code - https://github.com/insapathogenomics/algn2pheno
- findONTime - a tool to enable real-time metagenomics virus detection with the INSaFLU-TELEVIR platform
- Code - https://github.com/INSaFLU/findONTime
- FluMut - a bioinformatics tool for searching for molecular markers with potential impact on the biological characteristics of Influenza A viruses of the A(H5N1) subtype
- Web tool - https://izsvenezie-virology.github.io/FluMut/
- Code - https://github.com/izsvenezie-virology/FluMut
- Publication - https://doi.org/10.1093/ve/veaf011