diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 8fe75e8578a8..0da9c95b5c87 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,36 +1,36 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.89
+DISTVERSION=	2.5.90
 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 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 663d28cdcbe6..2c0ccc9928ee 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1765758525
-SHA256 (veg-hyphy-2.5.89_GH0.tar.gz) = 86db667a13ff559d6670b6caaf8063a4de3bfabef35313a825b6deaa1d640fdc
-SIZE (veg-hyphy-2.5.89_GH0.tar.gz) = 4372836
+TIMESTAMP = 1765759320
+SHA256 (veg-hyphy-2.5.90_GH0.tar.gz) = d11f7ce637c0683ffb253a4c371fd9ed9bdb70e5513fc4cb3c50546782012173
+SIZE (veg-hyphy-2.5.90_GH0.tar.gz) = 4372927