6 static bool Displayed = false;
\r
10 fprintf(stderr, "\n%s\n\n", MUSCLE_LONG_VERSION);
\r
11 fprintf(stderr, "http://www.drive5.com/muscle\n");
\r
12 fprintf(stderr, "This software is donated to the public domain.\n");
\r
13 fprintf(stderr, "Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.\n\n");
\r
24 " muscle -in <inputfile> -out <outputfile>\n"
\r
26 "Common options (for a complete list please see the User Guide):\n"
\r
28 " -in <inputfile> Input file in FASTA format (default stdin)\n"
\r
29 " -out <outputfile> Output alignment in FASTA format (default stdout)\n"
\r
30 " -diags Find diagonals (faster for similar sequences)\n"
\r
31 " -maxiters <n> Maximum number of iterations (integer, default 16)\n"
\r
32 " -maxhours <h> Maximum time to iterate in hours (default no limit)\n"
\r
33 " -html Write output in HTML format (default FASTA)\n"
\r
34 " -msf Write output in GCG MSF format (default FASTA)\n"
\r
35 " -clw Write output in CLUSTALW format (default FASTA)\n"
\r
36 " -clwstrict As -clw, with 'CLUSTAL W (1.81)' header\n"
\r
37 " -log[a] <logfile> Log to file (append if -loga, overwrite if -log)\n"
\r
38 " -quiet Do not write progress messages to stderr\n"
\r
39 " -version Display version information and exit\n"
\r
41 "Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2\n"
\r
42 "Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3\n"
\r
43 "Fastest possible (nucleotides): -maxiters 1 -diags\n");
\r