diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.43
+DISTVERSION=	2.5.46hf1
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
@@ -12,6 +12,7 @@
 ONLY_FOR_ARCHS=	aarch64 amd64 armv7 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
 
@@ -23,6 +24,6 @@
 
 AVX_CMAKE_OFF=	-DNOAVX:BOOL=ON
 
-# 2 tests fail, see https://github.com/veg/hyphy/issues/1529
+# All tests pass as of DISTVERSION=2.5.46hf1
 
 .include <bsd.port.mk>
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1672008666
-SHA256 (veg-hyphy-2.5.43_GH0.tar.gz) = 9328916267811a95dbbff94b51066dfc481f8d49ae0cf4d58e8384c58afbea50
-SIZE (veg-hyphy-2.5.43_GH0.tar.gz) = 5634198
+TIMESTAMP = 1673313088
+SHA256 (veg-hyphy-2.5.46hf1_GH0.tar.gz) = ec2f9e737741ce6811b7607b613b3c4be71e4ac57d0b516f0cb5174d8727be27
+SIZE (veg-hyphy-2.5.46hf1_GH0.tar.gz) = 5645952
diff --git a/biology/hyphy/files/patch-src_core_matrix.cpp b/biology/hyphy/files/patch-src_core_matrix.cpp
deleted file mode 100644
--- a/biology/hyphy/files/patch-src_core_matrix.cpp
+++ /dev/null
@@ -1,50 +0,0 @@
---- src/core/matrix.cpp.orig	2022-04-24 18:04:11 UTC
-+++ src/core/matrix.cpp
-@@ -3405,7 +3405,6 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix
-         #pragma GCC unroll 4
-         #pragma clang loop vectorize(enable)
-         #pragma clang loop interleave(enable)
--        #pragma clang loop unroll(enable)
-         #pragma GCC ivdep
-         #pragma ivdep
-                for (long idx = 0; idx < upto; idx+=16) {
-@@ -3909,7 +3908,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                                  #pragma GCC unroll 4
-                                  #pragma clang loop vectorize(enable)
-                                  #pragma clang loop interleave(enable)
--                                 #pragma clang loop unroll(enable)
-                                  for (long k = 0; k < vDim; k+=4) {
-                                       __m256d D4, B4;
-                                       DO_GROUP_OP (D4, B4, k);
-@@ -3960,7 +3958,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                                   #pragma GCC unroll 4
-                                   #pragma clang loop vectorize(enable)
-                                   #pragma clang loop interleave(enable)
--                                  #pragma clang loop unroll(enable)
-                                   for (long k = 0; k < vDim; k+=2) {
-                                       __m128d D4, B4;
-                                       DO_GROUP_OP1 (D4, B4, k);
-@@ -4177,7 +4174,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                             #pragma GCC unroll 4
-                             #pragma clang loop vectorize(enable)
-                             #pragma clang loop interleave(enable)
--                            #pragma clang loop unroll(enable)
-                               for (long k = 0; k < dimm4; k+=4) {
-                                   __m256d D4, B4;
-                                   DO_GROUP_OP (D4, B4, k);
-@@ -4285,7 +4281,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                                         #pragma GCC unroll 4
-                                         #pragma clang loop vectorize(enable)
-                                         #pragma clang loop interleave(enable)
--                                        #pragma clang loop unroll(enable)
-                                         for (long k = 0; k < dimm4; k+=2) {
-                                             __m128d D4, B4;
-                                             DO_GROUP_OP1 (D4, B4, k);
-@@ -4455,7 +4450,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                         #pragma GCC unroll 8
-                         #pragma clang loop vectorize(enable)
-                         #pragma clang loop interleave(enable)
--                        #pragma clang loop unroll(enable)
-                         for (long k = 0, column = j*hDim; k < vDim; k++, column ++) {
-                             resCell += row[k] * secondArg.theData [column];
-                         }