new version of muscle 3.8.31

[jabaws.git] / binaries / src / muscle / usage.cpp

diff --git a/binaries/src/muscle/usage.cpp b/binaries/src/muscle/usage.cpp
index 79b9d18..39a49f6 100644 (file)
--- a/binaries/src/muscle/usage.cpp
+++ b/binaries/src/muscle/usage.cpp
@@ -7,7 +7,7 @@ void Credits()
        if (Displayed)\r
                return;\r
 \r
-       fprintf(stderr, "\n" MUSCLE_LONG_VERSION "\n\n");\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
@@ -30,15 +30,12 @@ void Usage()
 "    -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
-"    -maxmb <m>         Maximum memory to allocate in Mb (default 80%% of RAM)\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
-"    -stable            Output sequences in input order (default is -group)\n"\r
-"    -group             Group sequences by similarity (this is the default)\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