--- /dev/null
+#ifndef _SRC_CLUSTAL_OMEGA_CONFIG_H
+#define _SRC_CLUSTAL_OMEGA_CONFIG_H 1
+
+/* src/clustal-omega-config.h. Generated automatically at end of configure. */
+/* src/config.h. Generated from config.h.in by configure. */
+/* src/config.h.in. Generated from configure.ac by autoheader. */
+
+/* Define if building universal (internal helper macro) */
+/* #undef AC_APPLE_UNIVERSAL_BUILD */
+
+/* Let all files know they are being used inside Clustal Omega */
+#ifndef CLUSTAL_OMEGA_CLUSTALO
+#define CLUSTAL_OMEGA_CLUSTALO 1
+#endif
+
+/* This is a CYGWIN system */
+/* #undef CYGWIN */
+
+/* This is a Darwin system */
+/* #undef DARWIN */
+
+/* Define to 1 if you have the <argtable2.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_ARGTABLE2_H
+#define CLUSTAL_OMEGA_HAVE_ARGTABLE2_H 1
+#endif
+
+/* Define to 1 if you have the <assert.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_ASSERT_H
+#define CLUSTAL_OMEGA_HAVE_ASSERT_H 1
+#endif
+
+/* Define to 1 if you have the <ctype.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_CTYPE_H
+#define CLUSTAL_OMEGA_HAVE_CTYPE_H 1
+#endif
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_DLFCN_H
+#define CLUSTAL_OMEGA_HAVE_DLFCN_H 1
+#endif
+
+/* Define to 1 if you have the <float.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_FLOAT_H
+#define CLUSTAL_OMEGA_HAVE_FLOAT_H 1
+#endif
+
+/* Define to 1 if you have the `fseek64' function. */
+/* #undef HAVE_FSEEK64 */
+
+/* Define to 1 if you have the `fseeko' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO
+#define CLUSTAL_OMEGA_HAVE_FSEEKO 1
+#endif
+
+/* Define to 1 if you have the `fseeko64' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO64
+#define CLUSTAL_OMEGA_HAVE_FSEEKO64 1
+#endif
+
+/* Define to 1 if you have the `ftell64' function. */
+/* #undef HAVE_FTELL64 */
+
+/* Define to 1 if you have the `ftello' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FTELLO
+#define CLUSTAL_OMEGA_HAVE_FTELLO 1
+#endif
+
+/* Define to 1 if you have the `ftello64' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FTELLO64
+#define CLUSTAL_OMEGA_HAVE_FTELLO64 1
+#endif
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_INTTYPES_H
+#define CLUSTAL_OMEGA_HAVE_INTTYPES_H 1
+#endif
+
+/* Define to 1 if you have the `argtable2' library (-largtable2). */
+#ifndef CLUSTAL_OMEGA_HAVE_LIBARGTABLE2
+#define CLUSTAL_OMEGA_HAVE_LIBARGTABLE2 1
+#endif
+
+/* Define to 1 if you have the `m' library (-lm). */
+#ifndef CLUSTAL_OMEGA_HAVE_LIBM
+#define CLUSTAL_OMEGA_HAVE_LIBM 1
+#endif
+
+/* Define to 1 if you have the <limits.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_LIMITS_H
+#define CLUSTAL_OMEGA_HAVE_LIMITS_H 1
+#endif
+
+/* Has log2() */
+#ifndef CLUSTAL_OMEGA_HAVE_LOG2
+#define CLUSTAL_OMEGA_HAVE_LOG2 1
+#endif
+
+/* Define to 1 if you have the <math.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_MATH_H
+#define CLUSTAL_OMEGA_HAVE_MATH_H 1
+#endif
+
+/* Define to 1 if you have the <memory.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_MEMORY_H
+#define CLUSTAL_OMEGA_HAVE_MEMORY_H 1
+#endif
+
+/* Define to 1 if you have the `ntohl' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_NTOHL
+#define CLUSTAL_OMEGA_HAVE_NTOHL 1
+#endif
+
+/* Define to 1 if you have the `ntohs' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_NTOHS
+#define CLUSTAL_OMEGA_HAVE_NTOHS 1
+#endif
+
+/* Define to 1 if you have the `ntonl' function. */
+/* #undef HAVE_NTONL */
+
+/* Define to 1 if you have the `ntons' function. */
+/* #undef HAVE_NTONS */
+
+/* Defined if OpenMP should and can be used */
+#ifndef CLUSTAL_OMEGA_HAVE_OPENMP
+#define CLUSTAL_OMEGA_HAVE_OPENMP 1
+#endif
+
+/* Define to 1 if you have the <stdarg.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDARG_H
+#define CLUSTAL_OMEGA_HAVE_STDARG_H 1
+#endif
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDINT_H
+#define CLUSTAL_OMEGA_HAVE_STDINT_H 1
+#endif
+
+/* Define to 1 if you have the <stdio.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDIO_H
+#define CLUSTAL_OMEGA_HAVE_STDIO_H 1
+#endif
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDLIB_H
+#define CLUSTAL_OMEGA_HAVE_STDLIB_H 1
+#endif
+
+/* Define to 1 if you have the <strings.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STRINGS_H
+#define CLUSTAL_OMEGA_HAVE_STRINGS_H 1
+#endif
+
+/* Define to 1 if you have the <string.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STRING_H
+#define CLUSTAL_OMEGA_HAVE_STRING_H 1
+#endif
+
+/* Define to 1 if you have the `stroul' function. */
+/* #undef HAVE_STROUL */
+
+/* Define to 1 if you have the `strtoull' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_STRTOULL
+#define CLUSTAL_OMEGA_HAVE_STRTOULL 1
+#endif
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_SYS_STAT_H
+#define CLUSTAL_OMEGA_HAVE_SYS_STAT_H 1
+#endif
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_SYS_TYPES_H
+#define CLUSTAL_OMEGA_HAVE_SYS_TYPES_H 1
+#endif
+
+/* Define to 1 if you have the <time.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_TIME_H
+#define CLUSTAL_OMEGA_HAVE_TIME_H 1
+#endif
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_UNISTD_H
+#define CLUSTAL_OMEGA_HAVE_UNISTD_H 1
+#endif
+
+/* This is a LINUX system */
+#ifndef CLUSTAL_OMEGA_LINUX
+#define CLUSTAL_OMEGA_LINUX 1
+#endif
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+ */
+#ifndef CLUSTAL_OMEGA_LT_OBJDIR
+#define CLUSTAL_OMEGA_LT_OBJDIR ".libs/"
+#endif
+
+/* This is a MinGW system */
+/* #undef MINGW */
+
+/* No-debug Mode */
+#ifndef CLUSTAL_OMEGA_NDEBUG
+#define CLUSTAL_OMEGA_NDEBUG /**/
+#endif
+
+/* Some strange OS */
+/* #undef OTHEROS */
+
+/* Name of package */
+#ifndef CLUSTAL_OMEGA_PACKAGE
+#define CLUSTAL_OMEGA_PACKAGE "clustal-omega"
+#endif
+
+/* Define to the address where bug reports for this package should be sent. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_BUGREPORT
+#define CLUSTAL_OMEGA_PACKAGE_BUGREPORT "clustalw@ucd.ie"
+#endif
+
+/* The package code name */
+#ifndef CLUSTAL_OMEGA_PACKAGE_CODENAME
+#define CLUSTAL_OMEGA_PACKAGE_CODENAME "DeshilHollesEamus"
+#endif
+
+/* Define to the full name of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_NAME
+#define CLUSTAL_OMEGA_PACKAGE_NAME "Clustal Omega"
+#endif
+
+/* Define to the full name and version of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_STRING
+#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.0.2"
+#endif
+
+/* Define to the one symbol short name of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_TARNAME
+#define CLUSTAL_OMEGA_PACKAGE_TARNAME "clustal-omega"
+#endif
+
+/* Define to the version of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION
+#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.0.2"
+#endif
+
+/* The size of `fpos_t', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T
+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16
+#endif
+
+/* The size of `unsigned int', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT 4
+#endif
+
+/* The size of `unsigned long', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8
+#endif
+
+/* The size of `unsigned long long', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG 8
+#endif
+
+/* The size of `unsigned short', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT 2
+#endif
+
+/* This is a Solaris system */
+/* #undef SOLARIS */
+
+/* This is a BSD system */
+/* #undef SOMEBSD */
+
+/* Define to 1 if you have the ANSI C header files. */
+#ifndef CLUSTAL_OMEGA_STDC_HEADERS
+#define CLUSTAL_OMEGA_STDC_HEADERS 1
+#endif
+
+/* Enable extensions on AIX 3, Interix. */
+#ifndef _ALL_SOURCE
+# define _ALL_SOURCE 1
+#endif
+/* Enable GNU extensions on systems that have them. */
+#ifndef _GNU_SOURCE
+# define _GNU_SOURCE 1
+#endif
+/* Enable threading extensions on Solaris. */
+#ifndef _POSIX_PTHREAD_SEMANTICS
+# define _POSIX_PTHREAD_SEMANTICS 1
+#endif
+/* Enable extensions on HP NonStop. */
+#ifndef _TANDEM_SOURCE
+# define _TANDEM_SOURCE 1
+#endif
+/* Enable general extensions on Solaris. */
+#ifndef __EXTENSIONS__
+# define __EXTENSIONS__ 1
+#endif
+
+
+/* Version number of package */
+#ifndef CLUSTAL_OMEGA_VERSION
+#define CLUSTAL_OMEGA_VERSION "1.0.2"
+#endif
+
+/* Define if using the dmalloc debugging malloc package */
+/* #undef WITH_DMALLOC */
+
+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
+ significant byte first (like Motorola and SPARC, unlike Intel). */
+#if defined AC_APPLE_UNIVERSAL_BUILD
+# if defined __BIG_ENDIAN__
+# define WORDS_BIGENDIAN 1
+# endif
+#else
+# ifndef WORDS_BIGENDIAN
+/* # undef WORDS_BIGENDIAN */
+# endif
+#endif
+
+/* Define to 1 if on MINIX. */
+/* #undef _MINIX */
+
+/* Define to 2 if the system does not provide POSIX.1 features except with
+ this defined. */
+/* #undef _POSIX_1_SOURCE */
+
+/* Define to 1 if you need to in order for `stat' and other things to work. */
+/* #undef _POSIX_SOURCE */
+
+/* Define to empty if `const' does not conform to ANSI C. */
+/* #undef const */
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+ calls it, or to nothing if 'inline' is not supported under any name. */
+#ifndef __cplusplus
+/* #undef inline */
+#endif
+
+/* Define to `long int' if <sys/types.h> does not define. */
+/* #undef off_t */
+
+/* Define to `unsigned int' if <sys/types.h> does not define. */
+/* #undef size_t */
+
+/* once: _SRC_CLUSTAL_OMEGA_CONFIG_H */
+#endif
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