Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / muscle / usage.cpp

diff --git a/website/archive/binaries/mac/src/muscle/usage.cpp b/website/archive/binaries/mac/src/muscle/usage.cpp
new file mode 100644 (file)
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+++ b/website/archive/binaries/mac/src/muscle/usage.cpp
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+#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