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diff --git a/sci-chemistry/tm-align/tm-align-20140601.ebuild b/sci-chemistry/tm-align/tm-align-20140601.ebuild
new file mode 100644
index 000000000000..e7718e305db1
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+++ b/sci-chemistry/tm-align/tm-align-20140601.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils flag-o-matic fortran-2
+
+DESCRIPTION="Quick & Accurate Structural Alignment"
+HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/TM-align/"
+SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz"
+
+LICENSE="tm-align"
+SLOT="0"
+KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux"
+IUSE="static custom-cflags"
+
+S="${WORKDIR}"
+
+src_prepare() {
+	cp "${FILESDIR}"/CMakeLists.txt . || die
+	use static && append-fflags -static && append-ldflags -static
+	# recommended by upstream
+	use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math
+}