This workshop provides on overview on phylogenetic analysis and interactive 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 and Basics
- Basics of phylogenetic analysis
- Exploring interactive phylogenies with Auspice
- The nextstrain toolchain
- Nextclade -- Analysis in the browser
- Analysis with augur and Snakemake -- Virus tutorial
Additional steps and details
- Options for time tree inference
- Specify color maps and geographic information
- Advanced snakemake (wildcards, functions, default rules)
- Parsing metadata from fasta files
Avian influenza resources
- Automatically updated analyses (by Louise Moncla and team). These exist for H5N1, H7N9, H9N2 as well as some broader ones like "H5Nx" that contain H5 viruses regardless of their neuraminidase segment. Most contain trees for all segments.
- Nextclade datasets for H5 clade 2.3.4.4
- Nextclade datasets for H5 clade 2.3.2.1
- Nextclade datasets for all H5 clades. See also Ort el al.
Newcastle Virus disease resources
There are no automatically updated phylogentic analyses available for NDV as of now (could be added if useful). But we have implemented Nextclade datasets for class-I and II. These are in their early stages and feedback in welcome.
Other relevant links
- nextstrain.org
- nextclade
- nextstrain documentation
- Example repository with zika sequences
- Time-scaled phylogenies with TreeTime
- installing conda
- snakemake tutorial