e2align2d

usage: prog <input> [options]

	Aligns a stack of particle images to a reference. If output is not specified, input file
	is overwritten with the aligned particles.

Option	Type	Description
--version	None	show program's version number and exit
--output	str	The name of the output class stack
--ref	str	Reference image to use for alignment. Required
--refn	int	Number of the reference image in 'ref'. Default=0
--align	str	This is the aligner used to align particles to the previous class average. Default is None.
--aligncmp	str	The comparitor used for the --align aligner. Default is dot.
--ralign	str	This is the second stage aligner used to refine the first alignment. This is usually the 'refine' aligner.
--raligncmp	str	The comparitor used by the second stage aligner.
--cmp	str	The comparitor used to generate quality scores for the purpose of particle exclusion in classes, strongly linked to the keep argument.
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness