This workshop provides on overview on phylogenetic analysis and dynamic visualization using nextstrain. Nextstrain is an open-source project to facilitate phylodynamic analysis, data integration, and visualization of large data sets of viral and bacterial pathogens. The analysis results can be visualized on your own computer or shared on the web.
Overview
- Basics of phylogenetic analysis
- Exploring interactive phylogenies with Auspice
- Analysis with augur and Snakemake -- viruses
- Analysis with augur and Snakemake -- bacteria
Important links
- nextstrain.org
- nextstrain documentation
- Time-scaled phylogenies with TreeTime
- getting miniconda
- snakemake tutorial