diff --git a/biology/muscle/files/patch-src__myutils.cpp b/biology/muscle/files/patch-src__myutils.cpp
index 68b2a4eacfed..75925719ba97 100644
--- a/biology/muscle/files/patch-src__myutils.cpp
+++ b/biology/muscle/files/patch-src__myutils.cpp
@@ -1,65 +1,60 @@
 --- myutils.cpp.orig	2022-01-13 23:29:59 UTC
 +++ myutils.cpp
-@@ -1050,7 +1050,62 @@
+@@ -1050,6 +1050,57 @@ double GetMemUseBytes()
  		g_PeakMemUseBytes = Bytes;
  	return Bytes;
  	}
 +#elif defined(__FreeBSD__)
 +
 +#include <sys/types.h>
 +#include <sys/sysctl.h>
 +#include <sys/user.h>
 +#include <unistd.h>
- 
++
 +double GetMemUseBytes()
 +	{
 +	static int initialized = 0;
 +	static int mib[4];
 +	static size_t len;
 +
 +	if (!initialized)
 +	{
 +		mib[0] = CTL_KERN;
 +		mib[1] = KERN_PROC;
 +		mib[2] = KERN_PROC_PID;
 +		mib[3] = getpid();
 +		len = sizeof(struct kinfo_proc);
 +		initialized = 1;
 +	}
 +
 +	struct kinfo_proc kp;
 +	if (sysctl(mib, 4, &kp, &len, NULL, 0) == -1)
 +		return 0.0;
 +
 +	// Resident set size in pages → convert to bytes
 +	long page_size = getpagesize();
 +	double bytes = (double)kp.ki_rssize * page_size;
 +
 +	if (bytes > g_PeakMemUseBytes)
 +		g_PeakMemUseBytes = bytes;
 +
 +	return bytes;
 +
 +	}
 +
 +double GetPhysMemBytes()
 +	{
-+ 	#if BITS == 32
-+	unsigned int physmem32 = 0;
-+	#else
-+	uint64_t physmem = 0;
-+	#endif
++	unsigned long physmem = 0;
 +
 +	size_t len = sizeof(physmem);
 +
 +	static int mib[2] = { CTL_HW, HW_PHYSMEM };
 +	if (sysctl(mib, 2, &physmem, &len, NULL, 0) == -1)
 +		return 0.0;
 +
 +	return (double)physmem;
 +
 +	}
-+
+ 
  #elif defined(__MACH__)
  #include <memory.h>
- #include <stdlib.h>
diff --git a/biology/muscle/files/patch-src__myutils.h b/biology/muscle/files/patch-src__myutils.h
new file mode 100644
index 000000000000..d39df958137e
--- /dev/null
+++ b/biology/muscle/files/patch-src__myutils.h
@@ -0,0 +1,11 @@
+--- myutils.h.orig	2026-08-29 19:37:51 UTC
++++ myutils.h
+@@ -11,7 +11,7 @@
+ #define TRACK_ALLOC		0
+ #define ALLOC_TOTALS	0
+ 
+-#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__)
++#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__LP64__)
+ #define	BITS			64
+ #else
+ #define	BITS			32
diff --git a/biology/muscle/files/patch-src__timing.h b/biology/muscle/files/patch-src__timing.h
new file mode 100644
index 000000000000..4d48299d0b47
--- /dev/null
+++ b/biology/muscle/files/patch-src__timing.h
@@ -0,0 +1,21 @@
+--- timing.h.orig	2026-08-29 19:42:39 UTC
++++ timing.h
+@@ -17,14 +17,14 @@ __inline__ uint64_t GetClockTicks()
+ 	}
+ 
+ #elif __GNUC__
++#include <time.h>
+ 
+ typedef uint64_t TICKS;
+ __inline__ uint64_t GetClockTicks()
+ 	{
+-	uint32_t lo, hi;
+-	/* We cannot use "=A", since this would use %rax on x86_64 */
+-	__asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi));
+-	return (uint64_t)hi << 32 | lo;
++	struct timespec ts;
++	clock_gettime(CLOCK_MONOTONIC, &ts);
++	return (uint64_t)ts.tv_sec * 1000000000 + ts.tv_nsec;
+ 	}
+ 
+ #else