A client-side WebAssembly pipeline for multi-sequence alignment and molecular clustering.
Visit: https://niema-lab.github.io/ViralWasm-Epi/ to run the pipeline.
Prerequisites: Python (Can be downloaded here: https://www.python.org/downloads/)
To run the pipeline locally without internet, download the zip file containing the offline mode of ViralWasm-Epi: https://github.com/Niema-Lab/ViralWasm-Epi/raw/master/viralwasm-epi-offline.zip. After, extract the folder, and click on the run_website.py file and select "Open with Python" for Windows or "Open With -> Python Launcher" for Mac.
Note: When starting the website for the first time offline, you may be prompted with a firewall warning. Click "Allow Access" to run the pipeline.
If you use ViralWasm-Epi in your work, please cite:
Ji D, Aboukhalil R, Moshiri N (2023). "ViralWasm: a client-side user-friendly web application suite for viral genomics." Bioinformatics. btae018. doi:10.1093/bioinformatics/btae018
Please also cite the following tools used in ViralWasm-Epi:
See https://biowasm.com/.
See https://github.com/pyodide/pyodide.
Moshiri N (2021). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics. 37(5):714–716. doi:10.1093/bioinformatics/btaa743
Li H (2018). "Minimap2: pairwise alignment for nucleotide sequences." Bioinformatics. 34(18):3094–3100. doi:10.1093/bioinformatics/bty191
See https://github.com/veg/tn93.
Tamura K, Nei M (1993). "Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees." Molecular Biology and Evolution. 10(3):512–526. doi:10.1093/oxfordjournals.molbev.a040023
Price MN, Dehal PS, Arkin AP (2010). "FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments." PLOS ONE. 5(3):e9490. doi:10.1371/journal.pone.0009490
See https://github.com/lh3/seqtk.
To TH, Jung M, Lycett S, Gascuel O (2016). "Fast dating using least-squares criteria and algorithms." Systematic Biology. 65(1):82–97. doi:10.1093/sysbio/syv068