Main tool: Augur
Definition: One held to foretell events by omens.
Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines.
The output of augur is a series of JSONs that can be used to visualize your results using Auspice.
Note: Auspice is a different tool.
augur index --sequences sequences.fasta --output sequence_index.tsv
augur filter \
--sequences data/sequences.fasta \
--sequence-index results/sequence_index.tsv \
--metadata data/metadata.tsv \
--exclude config/dropped_strains.txt \
--output results/filtered.fasta \
--group-by country year month \
--sequences-per-group 20 \
--min-date 2012
Better documentation can be found here.