diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile
index acde8f9f3f1c..0022e9cf09c4 100644
--- a/biology/gmap/Makefile
+++ b/biology/gmap/Makefile
@@ -1,31 +1,34 @@
 PORTNAME=	gmap
-PORTVERSION=	2020.09.12
+PORTVERSION=	2025.07.31
 CATEGORIES=	biology
 MASTER_SITES=	http://research-pub.gene.com/gmap/src/
 DISTNAME=	${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Genomic Mapping and Alignment Program for mRNA and EST Sequences
-WWW=		http://www.gene.com/share/gmap
+WWW=		https://github.com/genentech/gmap-gsnap \
+		http://research-pub.gene.com/gmap/
 
 LICENSE=	GMAP
 LICENSE_NAME=	GMAP License
 LICENSE_FILE=	${WRKSRC}/COPYING
 LICENSE_PERMS=	dist-mirror pkg-mirror auto-accept
 
+# FIXME: Source shows support for other platforms, but build fails on
+# aarch64 trying to use asm(bsr)
 ONLY_FOR_ARCHS=		amd64 i386 powerpc64le
-ONLY_FOR_ARCHS_REASON=	upstream supports only x86 and possibly POWER8
+ONLY_FOR_ARCHS_REASON=	Upstream supports only x86 and possibly POWER8
 
 USES=		gmake perl5
 GNU_CONFIGURE=	yes
 
 CONFLICTS_INSTALL=	cpuid scotch # bin/cpuid bin/gmap
 
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION:C|\.|-|g}
 CFLAGS+=	-fcommon
 
 OPTIONS_DEFINE=	SIMD
 
 SIMD_CONFIGURE_OFF=	--disable-builtin-popcount --disable-simd
 
 .include <bsd.port.mk>
diff --git a/biology/gmap/distinfo b/biology/gmap/distinfo
index 9ed16c632335..b02015bce13d 100644
--- a/biology/gmap/distinfo
+++ b/biology/gmap/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1600434673
-SHA256 (gmap-gsnap-2020-09-12.tar.gz) = 9f267d8d165a99b8cb41a22217ed9f8a987ba8b8f8303b0ae867d3e8bf96cef3
-SIZE (gmap-gsnap-2020-09-12.tar.gz) = 4470731
+TIMESTAMP = 1788268502
+SHA256 (gmap-gsnap-2025-07-31.tar.gz) = cc7212446683785a5b94aba79861212360d421ea409cd7cbf287f1dc63ed844d
+SIZE (gmap-gsnap-2025-07-31.tar.gz) = 5231678
diff --git a/biology/gmap/pkg-plist b/biology/gmap/pkg-plist
index 65b5bd55c23b..0ca75dba5798 100644
--- a/biology/gmap/pkg-plist
+++ b/biology/gmap/pkg-plist
@@ -1,39 +1,40 @@
 bin/atoiindex
 bin/cmetindex
 bin/cpuid
 bin/dbsnp_iit
 bin/ensembl_genes
 bin/fa_coords
 bin/get-genome
+bin/gff3_exons
 bin/gff3_genes
 bin/gff3_introns
 bin/gff3_splicesites
 bin/gmap
 bin/gmap.nosimd
 bin/gmap_build
 bin/gmap_cat
 bin/gmap_process
 bin/gmapindex
 bin/gmapl
 bin/gmapl.nosimd
 bin/gsnap
 bin/gsnap.nosimd
 bin/gsnapl
 bin/gsnapl.nosimd
+bin/gtf_exons
 bin/gtf_genes
 bin/gtf_introns
 bin/gtf_splicesites
 bin/gtf_transcript_splicesites
 bin/gvf_iit
 bin/iit_dump
 bin/iit_get
 bin/iit_store
 bin/indexdb_cat
 bin/md_coords
 bin/psl_genes
 bin/psl_introns
 bin/psl_splicesites
-bin/sam_sort
 bin/snpindex
 bin/trindex
 bin/vcf_iit