help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

alignment method

across

Multiple aligns sequence columns within groups and across rows using MUSCLE.

within

Multiple aligns sequence fields within rows using MUSCLE

block

Multiple aligns sequence groups across both columns and rows using MUSCLE.

output files:

align-pass

database with multiple aligned sequences.

align-fail

database with records failing alignment.

required fields:

sequence_id, v_call, j_call <field>

user specified sequence fields to align.

output fields:

<field>_align