The seqan-1.3.1-r1 ebuild is fine in this respect.
commit 6cd6d4f4e02a28fd020929485c88caaebc6b84c5 Author: David Seifert <soap@gentoo.org> Date: Sat Apr 9 20:23:54 2016 +0200 sci-biology/seqan: SLOT 1.4 and 2.1, allow for parallel installation Gentoo-Bug: 566502 * EAPI=6