getting rid of ambiguous documentation folder. all prog_doc are now stored in website...

[jabaws.git] / binaries / help / muscle3.7.txt

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-MUSCLE v3.7 by Robert C. Edgar\r
-\r
-http://www.drive5.com/muscle\r
-This software is donated to the public domain.\r
-Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.\r
-\r
-\r
-Basic usage\r
-\r
-    muscle -in <inputfile> -out <outputfile>\r
-\r
-Common options (for a complete list please see the User Guide):\r
-\r
-    -in <inputfile>    Input file in FASTA format (default stdin)\r
-    -out <outputfile>  Output alignment in FASTA format (default stdout)\r
-    -diags             Find diagonals (faster for similar sequences)\r
-    -maxiters <n>      Maximum number of iterations (integer, default 16)\r
-    -maxhours <h>      Maximum time to iterate in hours (default no limit)\r
-    -maxmb <m>         Maximum memory to allocate in Mb (default 80% of RAM)\r
-    -html              Write output in HTML format (default FASTA)\r
-    -msf               Write output in GCG MSF format (default FASTA)\r
-    -clw               Write output in CLUSTALW format (default FASTA)\r
-    -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header\r
-    -log[a] <logfile>  Log to file (append if -loga, overwrite if -log)\r
-    -quiet             Do not write progress messages to stderr\r
-    -stable            Output sequences in input order (default is -group)\r
-    -group             Group sequences by similarity (this is the default)\r
-    -version           Display version information and exit\r
-\r
-Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2\r
-Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3\r
-Fastest possible (nucleotides): -maxiters 1 -diags\r