help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

Alignment method

muscle

Align sequence sets using muscle.

offset

Align sequence sets using predefined 5' offset.

table

Create a 5' offset table by primer multiple alignment.

output files:

align-pass

multiple aligned reads.

align-fail

raw reads failing multiple alignment.

offsets-forward

5' offset table for input into offset subcommand.

offsets-reverse

3' offset table for input into offset subcommand.

output annotation fields:

None