READ_ALIGNMENT2 -- read 2nd alignment

FILE = $\langle{\tt string:1}\rangle$	'default'	partial or complete filename
DIRECTORY = $\langle{\tt string:1}\rangle$	''	directory list (e.g., 'dir1:dir2:dir3:./:/')
ALIGN_CODES2 = $\langle{\tt string:0}\rangle$	'all'	align codes for alignment2
ALIGNMENT_FORMAT = $\langle{\tt string:0}\rangle$	'PIR'	format of the alignment file: 'PIR' | 'PAP' | 'QUANTA' | 'INSIGHT' | 'FASTA'
REMOVE_GAPS = $\langle{\tt logical:1}\rangle$	on	whether to remove all-gap positions in input alignment
STOP_ON_ERROR = $\langle{\tt integer:1}\rangle$	1	whether to stop on error

Output:

MODELLER_STATUS = $\langle{\tt integer:1}\rangle$

Description:

This command reads the sequences and/or their alignment from a text file into the second alignment array. The two alignments can be compared by the COMPARE_ALIGNMENTS command.

Example: See READ_ALIGNMENT command.