diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index 4fac261c0913e..48e3770f13d91 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,2 +1 @@
-DIST bamtools-2.5.2.tar.gz 245729 BLAKE2B 5034ea1ec16b205488e421461ed74d8a98eae87eb7fc061e5928ad15512497a5338c9dbacbde51009c940acd55c25fccc2f3be2840d2821a8755a2a0b0370944 SHA512 540a4664abfbd1304600c17d47424c312a46e4238b0f0868f4037ddcc54c4487424e3d7820153084b3b512be8a4603e3ec5377a73311a617061460de1bfe49ef
 DIST bamtools-2.5.3.tar.gz 245648 BLAKE2B f387dd1dbae87ba22e811f81afd144d1c0fab02cd3c61f0442a3383a4f91d019a3ec8f0765e8d2ab8727bb9f1b3b22f4a2aff424a7c0aaa93396eb7afe0e9ba7 SHA512 bde9d98048d9f30d7f3c4e75db97e610ab58148dedadd09a36ad2421a6357b24510abda2451452d1fb9b40e22e1b8fe6f4e4c6ee1c529c426055a050a24b52d8
diff --git a/sci-biology/bamtools/bamtools-2.5.2-r1.ebuild b/sci-biology/bamtools/bamtools-2.5.2-r1.ebuild
deleted file mode 100644
index d1d591465a0bd..0000000000000
--- a/sci-biology/bamtools/bamtools-2.5.2-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
-else
-	SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0/${PV}" # no stable ABI yet
-
-RDEPEND="
-	>=dev-libs/jsoncpp-1.8.0:=
-	sys-libs/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/"${P}-cmake.patch" )
-
-src_prepare() {
-	# delete bundled libs, just to be safe
-	rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
-
-	cmake_src_prepare
-}
diff --git a/sci-biology/bamtools/bamtools-2.5.2.ebuild b/sci-biology/bamtools/bamtools-2.5.2.ebuild
deleted file mode 100644
index d972d243b9ff7..0000000000000
--- a/sci-biology/bamtools/bamtools-2.5.2.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
-else
-	SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0/${PV}" # no stable ABI yet
-
-RDEPEND="
-	>=dev-libs/jsoncpp-1.8.0:=
-	sys-libs/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	# delete bundled libs, just to be safe
-	rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
-
-	cmake_src_prepare
-}
diff --git a/sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch b/sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch
deleted file mode 100644
index d67efeeb4f7b9..0000000000000
--- a/sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Fix for CMake 4
-https://bugs.gentoo.org/951630
-https://github.com/pezmaster31/bamtools/commit/a610d2c0150d4b821aa4096e57eb77e4b0c14aa7
-From a610d2c0150d4b821aa4096e57eb77e4b0c14aa7 Mon Sep 17 00:00:00 2001
-From: David Seifert <SoapZA@users.noreply.github.com>
-Date: Sat, 31 Jul 2021 15:46:18 +0200
-Subject: [PATCH] CMakeLists.txt: CMake >= 3.11
-
-* `INCLUDE_GUARD_NAME` in `GENERATE_EXPORT_HEADER()` was added in 3.11
-
-Fixes: #216
----
- CMakeLists.txt | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index fc3a80c..2382802 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,4 +1,5 @@
--cmake_minimum_required(VERSION 3.0)
-+cmake_minimum_required(VERSION 3.11)
-+# need 3.11 for INCLUDE_GUARD_NAME in GENERATE_EXPORT_HEADER
- 
- project(
-     BamTools