===========================
Augur subcommands
===========================

You'll find documentation for all the augur subcommands below.
We're in the process of adding examples and more extensive documentation for each command, but at a minimum each subcommand will contain autogenerated documentation similar to that seen by running ``--help``.


.. toctree::
	:maxdepth: 1

	parse
	curate/index
	merge
	index
	filter
	subsample
	mask
	align
	tree
	refine
	ancestral
	translate
	reconstruct-sequences
	clades
	traits
	sequence-traits
	lbi
	distance
	titers
	frequencies
	export
	validate
	version
	import
	measurements
	read-file
	write-file