#define NULL ((void *)0)
typedef unsigned long size_t; // Customize by platform.
typedef long intptr_t;
typedef unsigned long uintptr_t;
typedef long scalar_t__; // Either arithmetic or pointer type.
/* By default, we understand bool (as a convenience). */
typedef int bool;
#define false 0
#define true 1

/* Forward declarations */

/* Type definitions */

/* Variables and functions */
int /*<<< orphan*/ printf(char *);
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;
}


x86 assembly (clang, -O0):
<NJ_usage>:
push   %rbp
mov    %rsp,%rbp
lea    0xee5(%rip),%rdi
call   1030 <printf@plt>
lea    0xf1d(%rip),%rdi
call   1030 <printf@plt>
lea    0xf23(%rip),%rdi
call   1030 <printf@plt>
lea    0xf47(%rip),%rdi
call   1030 <printf@plt>
lea    0xf74(%rip),%rdi
call   1030 <printf@plt>
lea    0xf9a(%rip),%rdi
call   1030 <printf@plt>
lea    0xfc4(%rip),%rdi
call   1030 <printf@plt>
lea    0x1000(%rip),%rdi
call   1030 <printf@plt>
lea    0x103b(%rip),%rdi
call   1030 <printf@plt>
lea    0x107b(%rip),%rdi
call   1030 <printf@plt>
lea    0x139f(%rip),%rdi
call   1030 <printf@plt>
lea    0x10b4(%rip),%rdi
call   1030 <printf@plt>
lea    0x10b8(%rip),%rdi
call   1030 <printf@plt>
lea    0x10d9(%rip),%rdi
call   1030 <printf@plt>
lea    0x1112(%rip),%rdi
call   1030 <printf@plt>
lea    0x1155(%rip),%rdi
call   1030 <printf@plt>
lea    0x1182(%rip),%rdi
call   1030 <printf@plt>
lea    0x134b(%rip),%rdi
call   1030 <printf@plt>
lea    0x11a7(%rip),%rdi
call   1030 <printf@plt>
lea    0x11e5(%rip),%rdi
call   1030 <printf@plt>
lea    0x122a(%rip),%rdi
call   1030 <printf@plt>
lea    0x131b(%rip),%rdi
call   1030 <printf@plt>
lea    0x1253(%rip),%rdi
call   1030 <printf@plt>
lea    0x1258(%rip),%rdi
call   1030 <printf@plt>
lea    0x127d(%rip),%rdi
call   1030 <printf@plt>
lea    0x12b5(%rip),%rdi
call   1030 <printf@plt>
lea    0x12e1(%rip),%rdi
call   1030 <printf@plt>
lea    0x1327(%rip),%rdi
call   1030 <printf@plt>
lea    0x12c7(%rip),%rdi
call   1030 <printf@plt>
lea    0x1361(%rip),%rdi
call   1030 <printf@plt>
lea    0x1360(%rip),%rdi
call   1030 <printf@plt>
lea    0x138c(%rip),%rdi
call   1030 <printf@plt>
lea    0x1297(%rip),%rdi
call   1030 <printf@plt>
lea    0x13aa(%rip),%rdi
call   1030 <printf@plt>
lea    0x13e6(%rip),%rdi
call   1030 <printf@plt>
pop    %rbp
ret

x86 assembly (clang, -O2):
<NJ_usage>:
push   %rax
lea    0xed8(%rip),%rdi
call   1040 <puts@plt>
lea    0xf0f(%rip),%rdi
call   1040 <puts@plt>
lea    0xf14(%rip),%rdi
call   1040 <puts@plt>
lea    0xf37(%rip),%rdi
call   1040 <puts@plt>
lea    0xf63(%rip),%rdi
call   1040 <puts@plt>
lea    0xf88(%rip),%rdi
call   1040 <puts@plt>
lea    0xfb1(%rip),%rdi
call   1040 <puts@plt>
lea    0xfec(%rip),%rdi
call   1040 <puts@plt>
lea    0x1026(%rip),%rdi
call   1040 <puts@plt>
lea    0x1065(%rip),%rdi
call   1040 <puts@plt>
mov    $0xa,%edi
call   1030 <putchar@plt>
lea    0x109f(%rip),%rdi
call   1040 <puts@plt>
lea    0x10a2(%rip),%rdi
call   1040 <puts@plt>
lea    0x10c2(%rip),%rdi
call   1040 <puts@plt>
lea    0x10fa(%rip),%rdi
call   1040 <puts@plt>
lea    0x113c(%rip),%rdi
call   1040 <puts@plt>
lea    0x1168(%rip),%rdi
call   1040 <puts@plt>
mov    $0xa,%edi
call   1030 <putchar@plt>
lea    0x118e(%rip),%rdi
call   1040 <puts@plt>
lea    0x11cb(%rip),%rdi
call   1040 <puts@plt>
lea    0x120f(%rip),%rdi
call   1040 <puts@plt>
mov    $0xa,%edi
call   1030 <putchar@plt>
lea    0x1239(%rip),%rdi
call   1040 <puts@plt>
lea    0x123d(%rip),%rdi
call   1040 <puts@plt>
lea    0x1261(%rip),%rdi
call   1040 <puts@plt>
lea    0x1298(%rip),%rdi
call   1040 <puts@plt>
lea    0x12c3(%rip),%rdi
call   1040 <puts@plt>
lea    0x1308(%rip),%rdi
call   1040 <puts@plt>
mov    $0xa,%edi
call   1030 <putchar@plt>
lea    0x1343(%rip),%rdi
call   1040 <puts@plt>
lea    0x1341(%rip),%rdi
call   1040 <puts@plt>
lea    0x136c(%rip),%rdi
call   1040 <puts@plt>
mov    $0xa,%edi
call   1030 <putchar@plt>
lea    0x138b(%rip),%rdi
call   1040 <puts@plt>
lea    0x13c6(%rip),%rdi
pop    %rax
jmp    1040 <puts@plt>

LLVM IR (-O0):
@.str = [68 x i8] c"Usage: clearcut --in=<infilename> --out=<outfilename> [options]...\0A\00"
@.str.1 = [18 x i8] c"GENERAL OPTIONS:\0A\00"
@.str.2 = [48 x i8] c" -h, --help Display this information.\0A\00"
@.str.3 = [57 x i8] c" -V, --version Print the version of this program.\0A\00"
@.str.4 = [50 x i8] c" -v, --verbose More output. (Default: OFF)\0A\00"
@.str.5 = [54 x i8] c" -q, --quiet Silent operation. (Default: ON)\0A\00"
@.str.6 = [72 x i8] c" -s, --seed=<seed> Explicitly set the PRNG seed to a specific value.\0A\00"
@.str.7 = [71 x i8] c" -r, --norandom Attempt joins deterministically. (Default: OFF)\0A\00"
@.str.8 = [76 x i8] c" -S, --shuffle Randomly shuffle the distance matrix. (Default: OFF)\0A\00"
@.str.9 = [81 x i8] c" -N, --neighbor Use traditional Neighbor-Joining algorithm. (Default: OFF)\0A\00"
@.str.10 = [2 x i8] c"\0A\00"
@.str.11 = [16 x i8] c"INPUT OPTIONS:\0A\00"
@.str.12 = [45 x i8] c" -I, --stdin Read input from STDIN.\0A\00"
@.str.13 = [69 x i8] c" -d, --distance Input file is a distance matrix. (Default: ON)\0A\00"
@.str.14 = [79 x i8] c" -a, --alignment Input file is a set of aligned sequences. (Default: OFF)\0A\00"
@.str.15 = [57 x i8] c" -D, --DNA Input alignment are DNA sequences.\0A\00"
@.str.16 = [61 x i8] c" -P, --protein Input alignment are protein sequences.\0A\00"
@.str.17 = [74 x i8] c"CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):\0A\00"
@.str.18 = [81 x i8] c" -j, --jukes Use Jukes-Cantor correction for computing distance matrix.\0A\00"
@.str.19 = [65 x i8] c" -k, --kimura Use Kimura correction for distance matrix.\0A\00"
@.str.20 = [17 x i8] c"OUTPUT OPTIONS:\0A\00"
@.str.21 = [49 x i8] c" -O, --stdout Output tree to STDOUT.\0A\00"
@.str.22 = [68 x i8] c" -m, --matrixout=<file> Output distance matrix to specified file.\0A\00"
@.str.23 = [56 x i8] c" -n, --ntrees=<n> Output n trees. (Default: 1)\0A\00"
@.str.24 = [82 x i8] c" -e, --expblen Exponential notation for branch lengths. (Default: OFF)\0A\00"
@.str.25 = [82 x i8] c" -E, --expdist Exponential notation in distance output. (Default: OFF)\0A\00"
@.str.26 = [11 x i8] c"EXAMPLES:\0A\00"
@.str.27 = [56 x i8] c" Compute tree by supplying distance matrix via stdin:\0A\00"
@.str.28 = [54 x i8] c" clearcut --distance < distances.txt > treefile.tre\0A\00"
@.str.29 = [72 x i8] c" Compute tree by supplying an alignment of DNA sequences from a file:\0A\00"
@.str.30 = [68 x i8] c" clearcut --alignment --DNA --in=alignment.txt --out=treefile.tre\0A\00"
define void @NJ_usage() {
%1 = call i32 @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str, i64 0, i64 0))
%2 = call i32 @printf(i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str.1, i64 0, i64 0))
%3 = call i32 @printf(i8* getelementptr inbounds ([48 x i8], [48 x i8]* @.str.2, i64 0, i64 0))
%4 = call i32 @printf(i8* getelementptr inbounds ([57 x i8], [57 x i8]* @.str.3, i64 0, i64 0))
%5 = call i32 @printf(i8* getelementptr inbounds ([50 x i8], [50 x i8]* @.str.4, i64 0, i64 0))
%6 = call i32 @printf(i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.5, i64 0, i64 0))
%7 = call i32 @printf(i8* getelementptr inbounds ([72 x i8], [72 x i8]* @.str.6, i64 0, i64 0))
%8 = call i32 @printf(i8* getelementptr inbounds ([71 x i8], [71 x i8]* @.str.7, i64 0, i64 0))
%9 = call i32 @printf(i8* getelementptr inbounds ([76 x i8], [76 x i8]* @.str.8, i64 0, i64 0))
%10 = call i32 @printf(i8* getelementptr inbounds ([81 x i8], [81 x i8]* @.str.9, i64 0, i64 0))
%11 = call i32 @printf(i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.10, i64 0, i64 0))
%12 = call i32 @printf(i8* getelementptr inbounds ([16 x i8], [16 x i8]* @.str.11, i64 0, i64 0))
%13 = call i32 @printf(i8* getelementptr inbounds ([45 x i8], [45 x i8]* @.str.12, i64 0, i64 0))
%14 = call i32 @printf(i8* getelementptr inbounds ([69 x i8], [69 x i8]* @.str.13, i64 0, i64 0))
%15 = call i32 @printf(i8* getelementptr inbounds ([79 x i8], [79 x i8]* @.str.14, i64 0, i64 0))
%16 = call i32 @printf(i8* getelementptr inbounds ([57 x i8], [57 x i8]* @.str.15, i64 0, i64 0))
%17 = call i32 @printf(i8* getelementptr inbounds ([61 x i8], [61 x i8]* @.str.16, i64 0, i64 0))
%18 = call i32 @printf(i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.10, i64 0, i64 0))
%19 = call i32 @printf(i8* getelementptr inbounds ([74 x i8], [74 x i8]* @.str.17, i64 0, i64 0))
%20 = call i32 @printf(i8* getelementptr inbounds ([81 x i8], [81 x i8]* @.str.18, i64 0, i64 0))
%21 = call i32 @printf(i8* getelementptr inbounds ([65 x i8], [65 x i8]* @.str.19, i64 0, i64 0))
%22 = call i32 @printf(i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.10, i64 0, i64 0))
%23 = call i32 @printf(i8* getelementptr inbounds ([17 x i8], [17 x i8]* @.str.20, i64 0, i64 0))
%24 = call i32 @printf(i8* getelementptr inbounds ([49 x i8], [49 x i8]* @.str.21, i64 0, i64 0))
%25 = call i32 @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str.22, i64 0, i64 0))
%26 = call i32 @printf(i8* getelementptr inbounds ([56 x i8], [56 x i8]* @.str.23, i64 0, i64 0))
%27 = call i32 @printf(i8* getelementptr inbounds ([82 x i8], [82 x i8]* @.str.24, i64 0, i64 0))
%28 = call i32 @printf(i8* getelementptr inbounds ([82 x i8], [82 x i8]* @.str.25, i64 0, i64 0))
%29 = call i32 @printf(i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.10, i64 0, i64 0))
%30 = call i32 @printf(i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.26, i64 0, i64 0))
%31 = call i32 @printf(i8* getelementptr inbounds ([56 x i8], [56 x i8]* @.str.27, i64 0, i64 0))
%32 = call i32 @printf(i8* getelementptr inbounds ([54 x i8], [54 x i8]* @.str.28, i64 0, i64 0))
%33 = call i32 @printf(i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.10, i64 0, i64 0))
%34 = call i32 @printf(i8* getelementptr inbounds ([72 x i8], [72 x i8]* @.str.29, i64 0, i64 0))
%35 = call i32 @printf(i8* getelementptr inbounds ([68 x i8], [68 x i8]* @.str.30, i64 0, i64 0))
ret void
}

LLVM IR (-O2):
@str = [67 x i8] c"Usage: clearcut --in=<infilename> --out=<outfilename> [options]...\00"
@str.31 = [17 x i8] c"GENERAL OPTIONS:\00"
@str.32 = [47 x i8] c" -h, --help Display this information.\00"
@str.33 = [56 x i8] c" -V, --version Print the version of this program.\00"
@str.34 = [49 x i8] c" -v, --verbose More output. (Default: OFF)\00"
@str.35 = [53 x i8] c" -q, --quiet Silent operation. (Default: ON)\00"
@str.36 = [71 x i8] c" -s, --seed=<seed> Explicitly set the PRNG seed to a specific value.\00"
@str.37 = [70 x i8] c" -r, --norandom Attempt joins deterministically. (Default: OFF)\00"
@str.38 = [75 x i8] c" -S, --shuffle Randomly shuffle the distance matrix. (Default: OFF)\00"
@str.39 = [80 x i8] c" -N, --neighbor Use traditional Neighbor-Joining algorithm. (Default: OFF)\00"
@str.40 = [15 x i8] c"INPUT OPTIONS:\00"
@str.41 = [44 x i8] c" -I, --stdin Read input from STDIN.\00"
@str.42 = [68 x i8] c" -d, --distance Input file is a distance matrix. (Default: ON)\00"
@str.43 = [78 x i8] c" -a, --alignment Input file is a set of aligned sequences. (Default: OFF)\00"
@str.44 = [56 x i8] c" -D, --DNA Input alignment are DNA sequences.\00"
@str.45 = [60 x i8] c" -P, --protein Input alignment are protein sequences.\00"
@str.46 = [73 x i8] c"CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):\00"
@str.47 = [80 x i8] c" -j, --jukes Use Jukes-Cantor correction for computing distance matrix.\00"
@str.48 = [64 x i8] c" -k, --kimura Use Kimura correction for distance matrix.\00"
@str.49 = [16 x i8] c"OUTPUT OPTIONS:\00"
@str.50 = [48 x i8] c" -O, --stdout Output tree to STDOUT.\00"
@str.51 = [67 x i8] c" -m, --matrixout=<file> Output distance matrix to specified file.\00"
@str.52 = [55 x i8] c" -n, --ntrees=<n> Output n trees. (Default: 1)\00"
@str.53 = [81 x i8] c" -e, --expblen Exponential notation for branch lengths. (Default: OFF)\00"
@str.54 = [81 x i8] c" -E, --expdist Exponential notation in distance output. (Default: OFF)\00"
@str.55 = [10 x i8] c"EXAMPLES:\00"
@str.56 = [55 x i8] c" Compute tree by supplying distance matrix via stdin:\00"
@str.57 = [53 x i8] c" clearcut --distance < distances.txt > treefile.tre\00"
@str.58 = [71 x i8] c" Compute tree by supplying an alignment of DNA sequences from a file:\00"
@str.59 = [67 x i8] c" clearcut --alignment --DNA --in=alignment.txt --out=treefile.tre\00"
define void @NJ_usage() {
%1 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str, i64 0, i64 0))
%2 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([17 x i8], [17 x i8]* @str.31, i64 0, i64 0))
%3 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([47 x i8], [47 x i8]* @str.32, i64 0, i64 0))
%4 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([56 x i8], [56 x i8]* @str.33, i64 0, i64 0))
%5 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([49 x i8], [49 x i8]* @str.34, i64 0, i64 0))
%6 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([53 x i8], [53 x i8]* @str.35, i64 0, i64 0))
%7 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([71 x i8], [71 x i8]* @str.36, i64 0, i64 0))
%8 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([70 x i8], [70 x i8]* @str.37, i64 0, i64 0))
%9 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([75 x i8], [75 x i8]* @str.38, i64 0, i64 0))
%10 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([80 x i8], [80 x i8]* @str.39, i64 0, i64 0))
%11 = tail call i32 @putchar(i32 10)
%12 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([15 x i8], [15 x i8]* @str.40, i64 0, i64 0))
%13 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([44 x i8], [44 x i8]* @str.41, i64 0, i64 0))
%14 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([68 x i8], [68 x i8]* @str.42, i64 0, i64 0))
%15 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([78 x i8], [78 x i8]* @str.43, i64 0, i64 0))
%16 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([56 x i8], [56 x i8]* @str.44, i64 0, i64 0))
%17 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([60 x i8], [60 x i8]* @str.45, i64 0, i64 0))
%18 = tail call i32 @putchar(i32 10)
%19 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([73 x i8], [73 x i8]* @str.46, i64 0, i64 0))
%20 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([80 x i8], [80 x i8]* @str.47, i64 0, i64 0))
%21 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([64 x i8], [64 x i8]* @str.48, i64 0, i64 0))
%22 = tail call i32 @putchar(i32 10)
%23 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([16 x i8], [16 x i8]* @str.49, i64 0, i64 0))
%24 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([48 x i8], [48 x i8]* @str.50, i64 0, i64 0))
%25 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str.51, i64 0, i64 0))
%26 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([55 x i8], [55 x i8]* @str.52, i64 0, i64 0))
%27 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([81 x i8], [81 x i8]* @str.53, i64 0, i64 0))
%28 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([81 x i8], [81 x i8]* @str.54, i64 0, i64 0))
%29 = tail call i32 @putchar(i32 10)
%30 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([10 x i8], [10 x i8]* @str.55, i64 0, i64 0))
%31 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([55 x i8], [55 x i8]* @str.56, i64 0, i64 0))
%32 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([53 x i8], [53 x i8]* @str.57, i64 0, i64 0))
%33 = tail call i32 @putchar(i32 10)
%34 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([71 x i8], [71 x i8]* @str.58, i64 0, i64 0))
%35 = tail call i32 @puts(i8* dereferenceable(1) getelementptr inbounds ([67 x i8], [67 x i8]* @str.59, i64 0, i64 0))
ret void
}