augur titers¶
Annotate a tree with actual and inferred titer measurements.
usage: augur titers [-h] {tree,sub} ...
Sub-commands:¶
tree¶
tree model
augur titers tree [-h] --titers TITERS [TITERS ...] --tree TREE
[--allow-empty-model] --output OUTPUT
Named Arguments¶
- --titers
file with titer measurements
- --tree, -t
tree to perform fit titer model to
- --allow-empty-model
allow model to be empty
Default: False
- --output, -o
JSON file to save titer model
sub¶
substitution model
augur titers sub [-h] --titers TITERS [TITERS ...] --alignment ALIGNMENT
[ALIGNMENT ...] --gene-names GENE_NAMES [GENE_NAMES ...]
[--tree TREE] [--allow-empty-model] --output OUTPUT
Named Arguments¶
- --titers
file with titer measurements
- --alignment
sequence to be used in the substitution model, supplied as fasta files
- --gene-names
names of the sequences in the alignment, same order assumed
- --tree, -t
optional tree to annotate fit titer model to
- --allow-empty-model
allow model to be empty
Default: False
- --output, -o
JSON file to save titer model