Using Augur

• Working with augur
• Augur command documentation
  • parse metadata from fasta-headers
  • Options of the refine command
    • Specify the evolutionary rate
    • Confidence intervals for divergence times
    • Specifying the root of the tree
    • Polytomy resolution
  • Labeling clades
  • Sub-commands:
    • parse
    • filter
    • mask
    • align
    • tree
    • refine
    • ancestral
    • translate
    • reconstruct-sequences
    • clades
    • traits
    • sequence-traits
    • lbi
    • distance
    • titers
    • frequencies
    • export
    • validate
    • version
• Augur and snakemake
• Format of augur output
• Environment variables