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