// File: /workspace/github_c_makefile_star2_O2/sheneman[P]clearcut/cmdargs.c
// Function: NJ_usage
void
NJ_usage(void) {
  
  printf("Usage: clearcut --in=<infilename> --out=<outfilename> [options]...\n");
  printf("GENERAL OPTIONS:\n");
  printf("  -h, --help         Display this information.\n");
  printf("  -V, --version      Print the version of this program.\n");
  printf("  -v, --verbose      More output. (Default: OFF)\n");
  printf("  -q, --quiet        Silent operation. (Default: ON)\n");
  printf("  -s, --seed=<seed>  Explicitly set the PRNG seed to a specific value.\n");
  printf("  -r, --norandom     Attempt joins deterministically.  (Default: OFF)\n");
  printf("  -S, --shuffle      Randomly shuffle the distance matrix.  (Default: OFF)\n");
  printf("  -N, --neighbor     Use traditional Neighbor-Joining algorithm. (Default: OFF)\n");

  printf("\n");
  printf("INPUT OPTIONS:\n");
  printf("  -I, --stdin        Read input from STDIN.\n");
  printf("  -d, --distance     Input file is a distance matrix. (Default: ON)\n");
  printf("  -a, --alignment    Input file is a set of aligned sequences. (Default: OFF)\n");
  printf("  -D, --DNA          Input alignment are DNA sequences.\n");
  printf("  -P, --protein      Input alignment are protein sequences.\n");

  printf("\n");
  printf("CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):\n");
  printf("  -j, --jukes        Use Jukes-Cantor correction for computing distance matrix.\n");
  printf("  -k, --kimura       Use Kimura correction for distance matrix.\n");
  
  printf("\n");
  printf("OUTPUT OPTIONS:\n");
  printf("  -O, --stdout           Output tree to STDOUT.\n");
  printf("  -m, --matrixout=<file> Output distance matrix to specified file.\n");
  printf("  -n, --ntrees=<n>       Output n trees.  (Default: 1)\n");
  printf("  -e, --expblen          Exponential notation for branch lengths. (Default: OFF)\n");
  printf("  -E, --expdist          Exponential notation in distance output. (Default: OFF)\n");
  
  printf("\n");
  printf("EXAMPLES:\n");
  printf("  Compute tree by supplying distance matrix via stdin:\n");
  printf("  clearcut --distance < distances.txt > treefile.tre\n");
  printf("\n");
  printf("  Compute tree by supplying an alignment of DNA sequences from a file:\n");
  printf("  clearcut --alignment --DNA --in=alignment.txt --out=treefile.tre\n");
  
  return;
}

// Assembly:
pushq %rbx
leaq 0x208b(%rip), %rdi      # 0x80e0
callq 0x20b0
leaq 0x20c2(%rip), %rdi      # 0x8123
callq 0x20b0
leaq 0x20c7(%rip), %rdi      # 0x8134
callq 0x20b0
leaq 0x20ea(%rip), %rdi      # 0x8163
callq 0x20b0
leaq 0x2116(%rip), %rdi      # 0x819b
callq 0x20b0
leaq 0x213b(%rip), %rdi      # 0x81cc
callq 0x20b0
leaq 0x2164(%rip), %rdi      # 0x8201
callq 0x20b0
leaq 0x219f(%rip), %rdi      # 0x8248
callq 0x20b0
leaq 0x21d9(%rip), %rdi      # 0x828e
callq 0x20b0
leaq 0x2218(%rip), %rdi      # 0x82d9
callq 0x20b0
pushq $0xa
popq %rbx
movl %ebx, %edi
callq 0x2050
leaq 0x2252(%rip), %rdi      # 0x8329
callq 0x20b0
leaq 0x2255(%rip), %rdi      # 0x8338
callq 0x20b0
leaq 0x2275(%rip), %rdi      # 0x8364
callq 0x20b0
leaq 0x22ad(%rip), %rdi      # 0x83a8
callq 0x20b0
leaq 0x22ef(%rip), %rdi      # 0x83f6
callq 0x20b0
leaq 0x231b(%rip), %rdi      # 0x842e
callq 0x20b0
movl %ebx, %edi
callq 0x2050
leaq 0x2344(%rip), %rdi      # 0x846a
callq 0x20b0
leaq 0x2381(%rip), %rdi      # 0x84b3
callq 0x20b0
leaq 0x23c5(%rip), %rdi      # 0x8503
callq 0x20b0
movl %ebx, %edi
callq 0x2050
leaq 0x23f2(%rip), %rdi      # 0x8543
callq 0x20b0
leaq 0x23f6(%rip), %rdi      # 0x8553
callq 0x20b0
leaq 0x241a(%rip), %rdi      # 0x8583
callq 0x20b0
leaq 0x2451(%rip), %rdi      # 0x85c6
callq 0x20b0
leaq 0x247c(%rip), %rdi      # 0x85fd
callq 0x20b0
leaq 0x24c1(%rip), %rdi      # 0x864e
callq 0x20b0
movl %ebx, %edi
callq 0x2050
leaq 0x24ff(%rip), %rdi      # 0x869f
callq 0x20b0
leaq 0x24fd(%rip), %rdi      # 0x86a9
callq 0x20b0
leaq 0x2528(%rip), %rdi      # 0x86e0
callq 0x20b0
movl %ebx, %edi
callq 0x2050
leaq 0x254a(%rip), %rdi      # 0x8715
callq 0x20b0
leaq 0x2585(%rip), %rdi      # 0x875c
popq %rbx
jmp 0x20b0