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