Running Bioinformatic Analyses
How-to guides for performing bioinformatic anaylses with Nextstrain.
Table of contents
- Manually Labeling Clades on a Nextstrain Tree
- Augur and snakemake
- Missing sequence data (gaps, indels, ambiguity)
- Finding a
translateandalignreference file - Importing BEAST MCC trees into augur
- Adding Custom Trait Colors
- Adding Custom Lat-Long Data
- Using VCF Input
- Using Fasta Input
- Inferring Sequence Traits (like Drug Resistance)
- Examples of Augur in the wild