diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 0e827bd9239e..162685dfa948 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,31 +1,36 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.77
-PORTREVISION=	1
+DISTVERSION=	2.5.88
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Hypothesis testing using Phylogenies
 WWW=		https://www.hyphy.org/ \
 		https://github.com/veg/hyphy/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 ONLY_FOR_ARCHS=	aarch64 amd64 i386 powerpc powerpc64 powerpc64le
 
 LIB_DEPENDS=	libcurl.so:ftp/curl
 TEST_DEPENDS=	bash:shells/bash
 
 USES=		cmake:insource,testing localbase:ldflags # tests fail in outsource build, see https://github.com/veg/hyphy/issues/1528
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	veg
 
-OPTIONS_DEFINE=		AVX TARGET_NATIVE
-AVX_DESC=		Advanced vector extensions support
-TARGET_NATIVE_DESC=	Enable CPU-specific instructions and tuning for build machine
+OPTIONS_DEFINE=		AVX FMA3 NEON SSE4 TARGET_NATIVE
+AVX_DESC=		Support for AVX (Advanced Vector Extensions) instructions
+FMA3_DESC=		Support for FMA3 (Fused Multiply-Add) instructions on x86
+NEON_DESC=		Support for NEON SIMD instructions on ARM
+SSE4_DESC=		Support for SSE4 (Streaming SIMD Extensions) instructions
+TARGET_NATIVE_DESC=	Enable CPU-specific optimizations for the build machine
 
 AVX_CMAKE_BOOL_OFF=		NOAVX
+FMA3_CMAKE_BOOL_OFF=		NOFMA3
+NEON_CMAKE_BOOL_OFF=		NONEON
+SSE4_CMAKE_BOOL_OFF=		NOSSE4
 TARGET_NATIVE_CMAKE_BOOL=	TARGET_NATIVE
 
 .include <bsd.port.mk>
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index 7a055e3a0004..7c94400e376d 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1755447505
-SHA256 (veg-hyphy-2.5.77_GH0.tar.gz) = 5012efd40938caeb9894bbd480565f95d735840f8eac67c6e84884a347e32e76
-SIZE (veg-hyphy-2.5.77_GH0.tar.gz) = 4027226
+TIMESTAMP = 1765067195
+SHA256 (veg-hyphy-2.5.88_GH0.tar.gz) = 0122f793fdf68599b96162dfea6a7fc34484c1d1a5dce8819d5b8d032878dba6
+SIZE (veg-hyphy-2.5.88_GH0.tar.gz) = 4372610
diff --git a/biology/hyphy/files/patch-src_core_global__things.cpp b/biology/hyphy/files/patch-src_core_global__things.cpp
deleted file mode 100644
index 397be8520ae5..000000000000
--- a/biology/hyphy/files/patch-src_core_global__things.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- src/core/global_things.cpp.orig	2025-08-22 19:21:44 UTC
-+++ src/core/global_things.cpp
-@@ -173,7 +173,7 @@ hyPointer MemAllocate(size_t bytes, bool zero, size_t 
-   result = (hyPointer)zero ? calloc(bytes, 1) : malloc(bytes);
- 
-   if (result == nil) {
--    HandleApplicationError(_String("Failed to allocate '") & bytes & "' bytes'",
-+    HandleApplicationError(_String("Failed to allocate '") & (unsigned long)bytes & "' bytes'",
-                            true);
-   }
-   return result;
-@@ -186,7 +186,7 @@ hyPointer MemReallocate(hyPointer old_pointer, size_t 
- 
-   if (result == nil) {
-     HandleApplicationError(
--        _String("Failed to resize memory to '") & new_size & "' bytes'", true);
-+        _String("Failed to resize memory to '") & (unsigned long)new_size & "' bytes'", true);
-   }
- 
-   return result;