Usage: maxalign.pl [-a] [-c=?] [-d] [-f=?] [-h=?] [-i=?] [-o[=?]] [-p] [-v=?] [-w] [-V] [<fastafile>] [<fastafile>]
   -a   All gaps columns in output is removed
   -c=? Char set used. All chars not in ? are considered gaps. Special; NUC = 4 nucleotides, and PROT = 20 amino acids.
   -d   Detailed report
   -f=? Prepends ? to output files. This could be a path and/or filename addition.
   -h=? Heuristic to use. Replace ? with 1-3. Default is 1 and that seems optimal.
   -i=? Iteratively removes up til ? sets until no improvement (0-999)
   -n   No gaps. Gaps (-) are considered a valid non-gap char. Only makes sense with -c option.
   -o=? Prove optimality in max ? minuts. 0 means no limit. Default is 5 min.
   -p   Pipe only the resulting alignment to STDOUT. No files - no fuss.
   -t=? Stop heuristic if improvement is not above threshold (in percent).
   -v=? Verbosity level (1-3). Default 0 - nothing
   -w   Web output
   -V   Version and copyright
Options must be given separately. If a fasta file is not given on command line,
then the alignment is expected as fasta on STDIN.
IFF two fasta files are given on command line then the optimal alignment area is
calculated for the first file, and the disturbing sequences from this calculation will
be removed from the second file, which would be output, i.e. the calculation will be
based on the first file, the effect on the second. This requires that the fasta IDs
are identical in both files. Used with amino acid and nucleotide fasta files - one each.
If a plus, +, is the first character in the sequence header (>+AC0023),
then that sequence is always included in the output. The + will be removed.
Possibly produces the output files; report.txt, heuristic.fsa, heuristic_include_headers.txt
heuristic_exclude_headers.txt, optimal.fsa, optimal_include_headers.txt and optimal_exclude_headers.txt