Commands may be entered in mixed case. All commands must include the '=' delimiter. All commands may use a maximum of 80 characters including their arguments, all commands are free format.
output_file=STRING STRING is the filename to be used for output of results and error messages. Must be the first command issued.
mode=OPTIONS OPTIONS are one of MULTIPLE, PAIRWISE or SCAN MULTIPLE is the default - signifies 'normal' multiple alignment and tree based alignments may be used. PAIRWISE signifies conventional pairwise comparisons to be made for all sequences in the seq_file. SCAN specifies that an alignment or pattern are to be compared to a group of sequences.
matrix_file=STRING STRING is the filename of the pairscore matrix chosen (one of MD.MAT, UP.MAT, GC.MAT etc)
seq_file=STRING STRING is the filename of the file containing sequences.
order_file=STRING STRING gives the name of the order file
constant=INT INT is a number added to each element of the matrix defined by matrix_file. (Default=8)
gap_penalty=REAL REAL is a number used as the length independent gap penalty. (Default=8.0).
iterations=INT INT defines the number of iterations performed in single order multiple alignment.
print_vertical= Switch to specify vertical format output of alignments.
print_horizontal= Switch to specify horizontal format output of alignments.
print_horizontal/pattern=STRING Specify creation of an output file with a suitable format for program PATT. STRING is the name of the file.
max_horiz=INT INT defines the number of residues output per line when the print_horizontal flag is set. (Default=100).
show_matrix= Flag to specify that the pairscore matrix should be written to the output file after any constant has been added.
block_file=STRING,INT Specifies the block_file name defined by STRING. INT specifies which iteration to read from the block_file. (INT MUST BE PRESENT OR AN ERROR WILL RESULT).
block_file/pattern=STRING,INT Specifies a block file with flexible pattern ranges.
consplot=OPTION Signals that a conservation profile should be plotted. Only works if the print_vertical command is set. OPTIONS are MZ for conservation profiles according to Zvelebil et al (1987). GB for a profile that is based upon the N*(N-1)/2 comparisons possible between all pairs of residues at a given alignment position.
gap_factor=REAL When aligning to a block_file, this command specifies the factor to be applied to the gap_penalty within the defined regions.
conscore= Flag to specify that the alignment will be scored using conservation values (a la Zvelebil et al 1987) instead of using the specified pairscore matrix.
show_lookup= Flag to specify that the lookup_table should be written out at each cycle of the alignment. The format produced cannot subsequently be read back in by the program.
save_lookup=STRING STRING is the name of a file to save the first generated lookup table to. Once saved, the program stops. The lookup table saved in this way may be read in by the program (see read_lookup) for subsequent processing.
s_lookup_comment=STRING May be used in conjunction with save_lookup to specify a title for the saved lookup Table.
read_lookup=STRING Defines the filename of a lookup table to be read in by the program. The Table overrides any table generated by pairscore matrices.
pairwise_random=INT1,INT2,INT3 Specifies the number of randomizations to be performed in pairwise per sequence pair in pairwise mode. INT1 = initial number of randomizations, INT2 = max number of randomizations, INT3 = increment. Normally one only requires a single value for randomizations - say 100. This would be defined thus: pairwise_random=100,100,1
pairwise_timer= Flag, if present then system statistics are recorded for each pairwise alignment.
pairwise_self= Flag, if present then in pairwise mode a self comparison is also made for each pair of sequences. (eg. for ABC, AvA, BvB etc.).
pairwise_align_file=STRING Specifies that alignments produced in pairwise mode be written to a file other than the output_file.
tree_file=STRING Specifies the name of the file containing the tree to follow for tree based multiple alignment. Also tells the program to perform a tree alignment rather than a single order alignment.
numerate= If print_vertical has been defined, then this will number each aligned position of the alignment.
non_alignment= Flag, signals that no alignment is performed. This can be useful to switch formats from vertical to horizontal, calculate conservation values or numerate the sequences. Note, if a block file is being read in then a seq_file must also be defined).
database,N= STRING
STRING specifies the name of the database to scan using the SCAN mode.
N specifies how many randomisations to perform for each database entry
- normally do not include a value for N (very expensive in CPU and not
very useful).
gap_char_dash= Specifies that all gaps will be output as dashes '-' rather than spaces.
gap_char_dot= Specifies that all gaps will be output as dots '.' rather than spaces.
use_end_pen= Weights gaps at the ends of the alignment (overhangs). Only effective in tree_file alignments.
last_it= In single order mode with multiple iterations, this requests that only the last iteration alignment is output. (Normally alignments for each iteration are displayed).
scanps_output= In scan mode, this outputs a more condensed version of the output file which only has a score, id pair on each line rather than the verbose output produced by default. This file must be sorted using the Unix sort utility rather than SORTER. (e.g. for a file called RESULTS.SCAN type: sort +0 -1 -n -r < RESULTS.SCAN > RESULTS.SORTED If you take the top N results from the .SORTED file, you can then extract the sequences using the SELECT program.