cutoff (-c <cutoff>): Sets the distance cutoff value, in Angstroms, for the final pass, which fills in some of the gaps. Cutoff can be any non-negative floating point number. This does not affect any of the bent files. The default value is 5.0 angstroms, which is what was used in the paper. A value of 0 prevents the last pass from running at all. Note that there should be a space after the c. P-values are calculated before the final extension pass, so the cutoff does no affect reported p-values.

Renumber (-r[01]): Disables or enables renumbering of all residues in all proteins. Each protein will start from residue 1 and all residues will be numbered consecutively. Insertion codes will be removed. Note that all loaded residues will be given a number, so if SEQRES entries are loaded or some residues have no alpha carbons, the first residue used in the alignment may not be residue 1. Disabled by default.

Rename (-l[01]): Disables or enables renaming chains in the output pdb files. When enabled, chains are first labeled by capital letters, then numbers, then symbols, then lowercase letters, and then the pattern repeats when there are over 90 chains. The limit is due to the fact that chains in a pdb file can only have a single character label. Chains are numbered according to the order they're specified in the command line. Enabled by default.

Read SEQRES(-s[01]): Disables or enables reading SEQRES lines in source pdb files. When enabled, the program tries to align residues in the ATOM entries to residues in the SEQRES entries. This allows detecting gaps between residues that would otherwise be assumed to be adjacent. Fragments cannot cross over regions with no alpha carbon coordinates. Note that residues with ATOM entries but no alpha carbons coordinate will always be loaded. When enabled, unalignable residues without alpha carbons will still appear in output files. -s also affects residue renumbering if -r is set. Enabled by default.

Verbose(-v[01]): Sets verbosity of feedback to stdout or log file. A value of 0 will only display errors and warnings, and 1 will display a list of chains as they are loaded. Default value is 1.

-d[01]: Disables or enables sending current progress to stderr. Current progress is either how many pairwise alignments are completed when running a single multiple alignment, or how many multiple alignments have been completed when running more than one multiple alignment at once. Enabled by default.

Partial(-p[01]): Disables or enables partial alignments. Has no effect on core residues and bent alignments. Partial alignment can have a very significant performance impact, particularly on alignments of large numbers of structures with few core residues. Enabled by default.

-t <thread count>: Sets the number of threads Matt uses. If not specified, Matt will use OpenMP's default number of threads, which is implementation dependent, though it is generally the number of threads a system is capable of running synchronously. When not compiled with OpenMP support, a warning will be displayed and the option will be ignored. Note that there should be a space between t and the number of threads.

-f <extension list>: Sets the output file formats to use. Extension list is case sensitive and must be comma-delimited and have no spaces. "all" is equivalent to listing all supported formats. The default value is "pdb,fasta,pdb,spt". The only other formats currently supported are msf, pir, and spdbv. When using -f, you must specify the default file formats again if you want them to be created, so "-f msf" would create no pdb files, for example.