// File: /workspace/github_c_makefile_star2_O3/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 %rax
leaq 0x2458(%rip), %rdi      # 0x9110
callq 0x20b0
leaq 0x248f(%rip), %rdi      # 0x9153
callq 0x20b0
leaq 0x2494(%rip), %rdi      # 0x9164
callq 0x20b0
leaq 0x24b7(%rip), %rdi      # 0x9193
callq 0x20b0
leaq 0x24e3(%rip), %rdi      # 0x91cb
callq 0x20b0
leaq 0x2508(%rip), %rdi      # 0x91fc
callq 0x20b0
leaq 0x2531(%rip), %rdi      # 0x9231
callq 0x20b0
leaq 0x256c(%rip), %rdi      # 0x9278
callq 0x20b0
leaq 0x25a6(%rip), %rdi      # 0x92be
callq 0x20b0
leaq 0x25e5(%rip), %rdi      # 0x9309
callq 0x20b0
movl $0xa, %edi
callq 0x2050
leaq 0x261f(%rip), %rdi      # 0x9359
callq 0x20b0
leaq 0x2622(%rip), %rdi      # 0x9368
callq 0x20b0
leaq 0x2642(%rip), %rdi      # 0x9394
callq 0x20b0
leaq 0x267a(%rip), %rdi      # 0x93d8
callq 0x20b0
leaq 0x26bc(%rip), %rdi      # 0x9426
callq 0x20b0
leaq 0x26e8(%rip), %rdi      # 0x945e
callq 0x20b0
movl $0xa, %edi
callq 0x2050
leaq 0x270e(%rip), %rdi      # 0x949a
callq 0x20b0
leaq 0x274b(%rip), %rdi      # 0x94e3
callq 0x20b0
leaq 0x278f(%rip), %rdi      # 0x9533
callq 0x20b0
movl $0xa, %edi
callq 0x2050
leaq 0x27b9(%rip), %rdi      # 0x9573
callq 0x20b0
leaq 0x27bd(%rip), %rdi      # 0x9583
callq 0x20b0
leaq 0x27e1(%rip), %rdi      # 0x95b3
callq 0x20b0
leaq 0x2818(%rip), %rdi      # 0x95f6
callq 0x20b0
leaq 0x2843(%rip), %rdi      # 0x962d
callq 0x20b0
leaq 0x2888(%rip), %rdi      # 0x967e
callq 0x20b0
movl $0xa, %edi
callq 0x2050
leaq 0x28c3(%rip), %rdi      # 0x96cf
callq 0x20b0
leaq 0x28c1(%rip), %rdi      # 0x96d9
callq 0x20b0
leaq 0x28ec(%rip), %rdi      # 0x9710
callq 0x20b0
movl $0xa, %edi
callq 0x2050
leaq 0x290b(%rip), %rdi      # 0x9745
callq 0x20b0
leaq 0x2946(%rip), %rdi      # 0x978c
popq %rax
jmp 0x20b0