PROF_TO_ALN -- profile to alignment

APPEND_ALN = <logical:1>

off

whether to append profiles to existing alignment arrays

Description:

This command will convert a profile that is in memory into the alignment format (see Section 2.4.1). The function of this command is complimentary to ALN_TO_PROF.

If the APPEND_ALN flag is set to 'on', then multiple profiles can be appended to the same alignment.

Note: Not all information of a 'PIR' format is encoded in a profile. (See READ_PROFILE). So converting a profile to an alignment may need manual attention to ensure that the alignment is useful for other routines.

Example:

# Example file for: READ_PROFILE, PROF_TO_ALN

# Read in the profile file
READ_PROFILE FILE = 'toxin.prf', PROFILE_FORMAT = 'TEXT'

# Convert the profile to alignment
PROF_TO_ALN

# Select the sequences to write out
SET ALIGN_CODES = '2ctx' '1nbt'

# Write out the alignment
WRITE_ALIGNMENT FILE = 'readprofile.pir', ALIGNMENT_FORMAT = 'PIR'