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diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild
new file mode 100644
index 000000000000..86183e7f9d3a
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+++ b/sci-biology/hmmer/hmmer-3.0.ebuild
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+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils
+
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+HOMEPAGE="http://hmmer.janelia.org/"
+SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+DEPEND="
+	mpi? ( virtual/mpi )
+	gsl? ( >=sci-libs/gsl-1.12 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-fix_tests.patch \
+		"${FILESDIR}"/${P}-perl-5.16-2.patch
+}
+
+src_configure() {
+	econf \
+		$(use_enable cpu_flags_x86_sse sse) \
+		$(use_enable mpi) \
+		$(use_enable threads) \
+		$(use_with gsl)
+}
+
+src_install() {
+	default
+
+	use static-libs && dolib.a src/libhmmer.a easel/libeasel.a
+
+	insinto /usr/share/${PN}
+	doins -r tutorial
+	dodoc Userguide.pdf
+}