diff --git a/sci-biology/mothur/ChangeLog b/sci-biology/mothur/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/mothur
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*mothur-1.36.1 (30 Nov 2015)
+
+  30 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/mothur-1.36.1-makefile.patch, +metadata.xml, +mothur-1.36.1.ebuild:
+  sci-biology/mothur: version bump; update makefile patch, the other patch from
+  1.27 series seems not necessary anymore; added few more IUSE values but the
+  makefile could ideally respect them before forcing boost and zlib libraries
+  into LIBS
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
@@ -0,0 +1 @@
+DIST mothur-1.36.1.tar.gz 1785450 SHA256 9dc1b78cc216dc333bb872e21d774ba0265820a3b75c10e1e68c3551d3e3b336 SHA512 c745efabbdc859f470b07d22266a3ad97fa81c011bc7ff1b705aa76d4d118ea81dfa58754f96e3172a393a29625e0aaa253252f76e442572fca869ccdc34b2ff WHIRLPOOL e5b4599374453f24a5798c4f56dc8d89b9fd6c2db30e43ec919ac9af1cb8b978d3cab2cfd2de8da83bcf8f7d0d0040c719e6b7e79f35a99590c3918ddf99cfc0
diff --git a/sci-biology/mothur/files/mothur-1.36.1-makefile.patch b/sci-biology/mothur/files/mothur-1.36.1-makefile.patch
@@ -0,0 +1,61 @@
+--- mothur-1.36.1/makefile.ori	2015-11-30 18:38:40.511576683 +0100
++++ mothur-1.36.1/makefile	2015-11-30 18:41:24.261579412 +0100
+@@ -9,7 +9,7 @@
+ #
+
+ USEMPI ?= no
+-64BIT_VERSION ?= yes
++64BIT_VERSION ?= no
+ USEREADLINE ?= yes
+ USECOMPRESSION ?= no
+ USEBOOST ?= yes
+@@ -18,7 +18,7 @@
+ VERSION = "\"1.36.1\""
+
+ # Optimize to level 3:
+-CXXFLAGS += -O3
++# CXXFLAGS += -O3
+
+
+ ifeq  ($(strip $(64BIT_VERSION)),yes)
+@@ -58,7 +58,7 @@
+
+
+ ifeq  ($(strip $(USEMPI)),yes)
+-    CXX = mpic++
++#    CXX = mpic++
+     CXXFLAGS += -DUSE_MPI
+ endif
+
+@@ -106,10 +106,8 @@
+     OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+
+-mothur : $(OBJECTS) uchime
++mothur : $(OBJECTS)
+ 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+-	strip mothur
+-
+
+ uchime:
+ 	cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
+--- mothur-1.36.1/makefile.ori	2015-11-30 18:46:41.411584697 +0100
++++ mothur-1.36.1/makefile	2015-11-30 19:15:18.531613315 +0100
+@@ -64,14 +64,12 @@
+
+ #The boost libraries allow you to read gz files.
+ ifeq  ($(strip $(USEBOOST)),yes)
+-    BOOST_INCLUDE_DIR="/usr/local/include"
+-    BOOST_LIBRARY_DIR="/usr/local/lib"
++    BOOST_INCLUDE_DIR="/usr/include"
++    BOOST_LIBRARY_DIR="/usr/lib"
+
+     CXXFLAGS += -DUSE_BOOST
+
+-    LIBS += \
+-    ${BOOST_LIBRARY_DIR}/libboost_iostreams.a \
+-    ${BOOST_LIBRARY_DIR}/zlib.a
++    LIBS += -lboost_iostreams -lz
+
+     #if linux or windows then ${BOOST_LIBRARY_DIR}/libz.a
+ endif
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mothur/mothur-1.36.1.ebuild b/sci-biology/mothur/mothur-1.36.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite of algorithms for ecological bioinformatics"
+HOMEPAGE="http://www.mothur.org/"
+SRC_URI="https://github.com/mothur/mothur/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="mpi readline zlib"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-libs/boost"
+RDEPEND="
+	sci-biology/uchime
+	mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX)
+	use amd64 && append-cppflags -DBIT_VERSION
+	use readline && export USEREADLINE=yes || export USEREADLINE=no
+	# use boost && export USEBOOST=yes || export USEBOOST=no
+	use zlib && export USECOMPRESSION=yes || export USECOMPRESSION=no
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-makefile.patch \
+#		"${FILESDIR}"/${PN}-1.27.0-overflows.patch
+}
+
+src_compile() {
+	emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) USEBOOST=$(usex boost) USECOMPRESSION=$(usex zlib)
+}
+
+src_install() {
+	dobin ${PN}
+}
diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/repeatmasker-4.0.6__configure.patch,
+  -files/RepeatMasker-open-4-0-1__configure.patch,
+  -files/RepeatMasker-open-4-0-6__configure.patch:
+  sci-biology/repeatmasker: rename and move the patch file; drop old patch for a
+  previous version
+
   24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   repeatmasker-4.0.1-r1.ebuild:
   sci-biology/repeatmasker: improve einfo message

diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
@@ -1 +1 @@
-DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77
+DIST RepeatMasker-open-4-0-6.tar.gz 266192837 SHA256 778ecd988a0afbe90318c3e9c597f16ae46da593af5f94db9d05f8c30d6cfd44 SHA512 3ca3593a736ab3741c01cfc79e6bdce0ff069cdd12e7e98864b4feeabf93422247aebaf0305d2121b99fd08166be2f7cc443080a2966331dc7f4c45b800a8a97 WHIRLPOOL 24a9beef75215b3517183755bbe13d30a5f954eb74471705a15ce3f974f0b63fe836a62ff8f0f5ef99e72b27738d5888ce5f35379b90e72eb627031836ffcaf7
diff --git a/...iology/repeatmasker/files/configure.patch → ...files/repeatmasker-4.0.6__configure.patch b/...iology/repeatmasker/files/configure.patch → ...files/repeatmasker-4.0.6__configure.patch
@@ -1,5 +1,5 @@
---- configure.ori	2013-02-21 02:32:30.000000000 +0100
-+++ configure	2015-11-24 19:54:50.630202150 +0100
+--- configure.ori	2015-11-24 20:56:46.000000000 +0100
++++ configure	2015-11-24 20:59:58.000000000 +0100
 @@ -253,17 +253,16 @@
    close INVERS;
  }
@@ -67,16 +67,16 @@
 
    my $wuDefault = &promptScreen(
      "",
-@@ -748,7 +747,7 @@
-         }
+@@ -756,7 +755,7 @@
        }
-       else {
--        print "ERROR: Could not find nhmmer program in this directory!\n";
-+        print "ERROR: Could not find nhmmer program in '$location' directory!\n";
-       }
-       if ( $goodParam == 0 ) {
-         print "<PRESS ENTER TO CONTINUE>\n";
-@@ -773,7 +772,7 @@
+     }
+     else {
+-      print "ERROR: Could not find nhmmer program in this directory!\n";
++      print "ERROR: Could not find nhmmer program in '$location' directory!\n";
+     }
+   }
+
+@@ -776,7 +775,7 @@
    }
    close IN;
    close OUT;
@@ -85,7 +85,7 @@
 
    my $default = &promptScreen(
      "",
-@@ -827,7 +826,7 @@
+@@ -830,7 +829,7 @@
    }
    close IN;
    close OUT;
@@ -94,7 +94,7 @@
 
    my $deDefault = &promptScreen(
      "",
-@@ -863,9 +862,6 @@
+@@ -866,9 +865,6 @@
 
    my $answer = undef;
 
@@ -104,19 +104,3 @@
    print "\n\n\n";
    print $screenText;
    my $numLines = ( $screenText =~ s/(\n)/$1/g );
---- configure.ori	2015-11-24 20:10:58.640204679 +0100
-+++ configure	2015-11-24 20:11:00.970204685 +0100
-@@ -728,11 +728,12 @@
-         # HMMER 3.0dev (March 2010); http://hmmer.org/
-         # HMMER 3.1dev_0.33 (July 2012); http://hmmer.org
-         # HMMER hmmer3.1-snap20120830 (August 2012); http://hmmer.org/
-+	# HMMER 3.1b2 (February 2015); http://hmmer.org/
-         while ( $result =~ /([^\n\r]*)[\n\r]/ig ) {
-           my $line = $1;
-
-           if ( $line =~ /^#\s+HMMER\s+(\d+\.\d+)((dev)?(_\d+\.\d+)?\s+\(.*\)).*/
--               || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ )
-+               || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ || $line =~ /^#\s+HMMER\s+(\d+\.\d+).*/)
-           {
-             if ( $1 >= 3.1 ) {
-               $goodParam = 1;
diff --git a/...repeatmasker/repeatmasker-4.0.1-r1.ebuild → ...gy/repeatmasker/repeatmasker-4.0.6.ebuild b/...repeatmasker/repeatmasker-4.0.1-r1.ebuild → ...gy/repeatmasker/repeatmasker-4.0.6.ebuild
@@ -28,7 +28,7 @@ RDEPEND="
 S="${WORKDIR}/RepeatMasker"
 
 src_prepare(){
-	epatch "${FILESDIR}"/configure.patch
+	epatch "${FILESDIR}"/"${P}"__configure.patch
 }
 
 src_configure() {
@@ -37,11 +37,11 @@ src_configure() {
 	#  -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
 	# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
 	sed -i -e 's/system( "clear" );//' "${S}/configure" || die
-	mkdir -p ${D}//usr/share/repeatmasker/Libraries/ || die
+	mkdir -p "${D}"/usr/share/repeatmasker/Libraries/ || die
 	#
 	# the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
 	# item does not get installed
-	echo ">blah\natgc" > ${D}//usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+	echo ">blah\natgc" > "${D}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
 	# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
 	echo "
 env

diff --git a/sci-libs/lapack-reference/lapack-reference-3.6.0.ebuild b/sci-libs/lapack-reference/lapack-reference-3.6.0.ebuild
@@ -20,7 +20,7 @@ SRC_URI="http://www.netlib.org/lapack/${MYP}.tgz"
 LICENSE="BSD"
 SLOT="0/${PV}"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs test xblas"
+IUSE="+deprecated static-libs test xblas"
 
 REQUIRED_USE="test? ( ${PYTHON_REQUIRED_USE} )"
 
@@ -82,6 +82,7 @@ src_configure() {
 			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${blas_profname})"
 			$(cmake-utils_use_build test TESTING)
 			$(cmake-utils_use_use xblas XBLAS)
+			$(cmake-utils_use_build deprecated DEPRECATED)
 			-DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CFLAGS}"
 			-DCMAKE_CXX_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) ${CXXFLAGS}"
 			-DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags ${blas_profname}) $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags) ${FCFLAGS}"

diff --git a/sci-libs/lapack-reference/metadata.xml b/sci-libs/lapack-reference/metadata.xml
@@ -13,8 +13,10 @@
   Algebra Subprogram (BLAS).
 </longdescription>
   <use>
+    <flag name="deprecated">Build deprecated routines</flag>
     <flag name="int64">Build the 64 bits integer library</flag>
-    <flag name="xblas">Build LAPACK with extra precision (needs
-  <pkg>sci-libs/xblas</pkg>)</flag>
+    <flag name="xblas">
+    	Build LAPACK with extra precision (needs <pkg>sci-libs/xblas</pkg>)
+    </flag>
   </use>
 </pkgmetadata>