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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
.TH AUGUR "1" "June 2022" "augur 16.0.1" "User Commands"
.SH NAME
augur \- pipeline components for real-time virus analysis
.SH DESCRIPTION
usage: augur [\-h]
.IP
{parse, index, filter, mask, align, tree, refine, ancestral, translate, reconstruct\-sequences, clades, traits, sequence\-traits, lbi, distance, titers, frequencies, export, validate, version, import, measurements}
\&...
.PP
Augur: A bioinformatics toolkit for phylogenetic analysis.
.SS "positional arguments:"
.IP
{parse, index, filter, mask, align, tree, refine, ancestral, translate, reconstruct\-sequences, clades, traits, sequence\-traits, lbi, distance, titers, frequencies, export, validate, version, import, measurements}
.TP
parse
Parse delimited fields from FASTA sequence names into
a TSV and FASTA file.
.TP
index
Count occurrence of bases in a set of sequences.
.TP
filter
Filter and subsample a sequence set.
.TP
mask
Mask specified sites from a VCF or FASTA file.
.TP
align
Align multiple sequences from FASTA.
.TP
tree
Build a tree using a variety of methods.
.TP
refine
Refine an initial tree using sequence metadata.
.TP
ancestral
Infer ancestral sequences based on a tree.
.TP
translate
Translate gene regions from nucleotides to amino
acids.
.TP
reconstruct\-sequences
Reconstruct alignments from mutations inferred on the
tree
.TP
clades
Assign clades to nodes in a tree based on amino\-acid
or nucleotide signatures.
.TP
traits
Infer ancestral traits based on a tree.
.TP
sequence\-traits
Annotate sequences based on amino\-acid or nucleotide
signatures.
.TP
lbi
Calculate LBI for a given tree and one or more sets of
parameters.
.TP
distance
Calculate the distance between sequences across entire
genes or at a predefined subset of sites.
.TP
titers
Annotate a tree with actual and inferred titer
measurements.
.TP
frequencies
infer frequencies of mutations or clades
.TP
export
Export JSON files suitable for visualization with
auspice.
.TP
validate
Validate files related to augur consumption or export.
.TP
version
Print the version of augur.
.TP
import
Import analyses into augur pipeline from other systems
.TP
measurements
Create JSON files suitable for visualization within
the measurements panel of Auspice.
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SH AUTHOR
This manpage was written by Étienne Mollier for the Debian distribution and can be used for any other usage of the program.
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