diff --git a/Makefile.in b/Makefile.in
index b8e5c3d8..2370643b 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.15.1 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2014 Free Software Foundation, Inc.
+# Copyright (C) 1994-2017 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -3447,7 +3447,7 @@ distdir: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
@@ -3473,7 +3473,7 @@ dist-shar: distdir
 	@echo WARNING: "Support for shar distribution archives is" \
 	               "deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)
 
 dist-zip: distdir
@@ -3491,7 +3491,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -3501,7 +3501,7 @@ distcheck: dist
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac
diff --git a/aclocal.m4 b/aclocal.m4
index 3d25452b..14241828 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,6 +1,6 @@
-# generated automatically by aclocal 1.15 -*- Autoconf -*-
+# generated automatically by aclocal 1.15.1 -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2017 Free Software Foundation, Inc.
 
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically 'autoreconf'.])])
 
-# Copyright (C) 2002-2014 Free Software Foundation, Inc.
+# Copyright (C) 2002-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -35,7 +35,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],
 [am__api_version='1.15'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15], [],
+m4_if([$1], [1.15.1], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -51,12 +51,12 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15])dnl
+[AM_AUTOMAKE_VERSION([1.15.1])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
-# Copyright (C) 2011-2014 Free Software Foundation, Inc.
+# Copyright (C) 2011-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -118,7 +118,7 @@ AC_SUBST([AR])dnl
 
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -170,7 +170,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd`
 
 # AM_CONDITIONAL                                            -*- Autoconf -*-
 
-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -201,7 +201,7 @@ AC_CONFIG_COMMANDS_PRE(
 Usually this means the macro was only invoked conditionally.]])
 fi])])
 
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -392,7 +392,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
 
 # Generate code to set up dependency tracking.              -*- Autoconf -*-
 
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -468,7 +468,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
 
 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -665,7 +665,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -686,7 +686,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])
 
-# Copyright (C) 2003-2014 Free Software Foundation, Inc.
+# Copyright (C) 2003-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -708,7 +708,7 @@ AC_SUBST([am__leading_dot])])
 # Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-
 # From Jim Meyering
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -743,7 +743,7 @@ AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
 
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -793,7 +793,7 @@ rm -f confinc confmf
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -832,7 +832,7 @@ fi
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -861,7 +861,7 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
 
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -908,7 +908,7 @@ AC_LANG_POP([C])])
 # For backward compatibility.
 AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -927,7 +927,7 @@ AC_DEFUN([AM_RUN_LOG],
 
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1008,7 +1008,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])
 
-# Copyright (C) 2009-2014 Free Software Foundation, Inc.
+# Copyright (C) 2009-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1068,7 +1068,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1096,7 +1096,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2014 Free Software Foundation, Inc.
+# Copyright (C) 2006-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1115,7 +1115,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004-2014 Free Software Foundation, Inc.
+# Copyright (C) 2004-2017 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
diff --git a/configure b/configure
index 950be27c..ac6c3eca 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for cosi 2.0.
+# Generated by GNU Autoconf 2.69 for cosi 2.3.0-beta.1.
 #
 # Report bugs to <ilya_shl@alum.mit.edu>.
 #
@@ -536,14 +536,14 @@ if (echo >conf$$.file) 2>/dev/null; then
     # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
     # In both cases, we have to default to `cp -pR'.
     ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp --preserve=timestamps -R'
+      as_ln_s='cp -pR'
   elif ln conf$$.file conf$$ 2>/dev/null; then
     as_ln_s=ln
   else
-    as_ln_s='cp --preserve=timestamps -R'
+    as_ln_s='cp -pR'
   fi
 else
-  as_ln_s='cp --preserve=timestamps -R'
+  as_ln_s='cp -pR'
 fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='cosi'
 PACKAGE_TARNAME='cosi'
-PACKAGE_VERSION='2.0'
-PACKAGE_STRING='cosi 2.0'
+PACKAGE_VERSION='2.3.0-beta.1'
+PACKAGE_STRING='cosi 2.3.0-beta.1'
 PACKAGE_BUGREPORT='ilya_shl@alum.mit.edu'
 PACKAGE_URL=''
 
@@ -1366,7 +1366,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures cosi 2.0 to adapt to many kinds of systems.
+\`configure' configures cosi 2.3.0-beta.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1436,7 +1436,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of cosi 2.0:";;
+     short | recursive ) echo "Configuration of cosi 2.3.0-beta.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1556,7 +1556,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-cosi configure 2.0
+cosi configure 2.3.0-beta.1
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2051,7 +2051,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by cosi $as_me 2.0, which was
+It was created by cosi $as_me 2.3.0-beta.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2915,7 +2915,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='cosi'
- VERSION='2.0'
+ VERSION='2.3.0-beta.1'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -17054,14 +17054,14 @@ if (echo >conf$$.file) 2>/dev/null; then
     # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
     # In both cases, we have to default to `cp -pR'.
     ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp --preserve=timestamps -R'
+      as_ln_s='cp -pR'
   elif ln conf$$.file conf$$ 2>/dev/null; then
     as_ln_s=ln
   else
-    as_ln_s='cp --preserve=timestamps -R'
+    as_ln_s='cp -pR'
   fi
 else
-  as_ln_s='cp --preserve=timestamps -R'
+  as_ln_s='cp -pR'
 fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
@@ -17151,7 +17151,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by cosi $as_me 2.0, which was
+This file was extended by cosi $as_me 2.3.0-beta.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -17208,7 +17208,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-cosi config.status 2.0
+cosi config.status 2.3.0-beta.1
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
diff --git a/configure.ac b/configure.ac
index fb2f847f..8419c513 100644
--- a/configure.ac
+++ b/configure.ac
@@ -5,7 +5,7 @@
 #
 
 AC_PREREQ([2.68])
-AC_INIT([cosi], [2.0], [ilya_shl@alum.mit.edu])
+AC_INIT([cosi], [2.3.0-beta.1], [ilya_shl@alum.mit.edu])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([1.9 tar-pax parallel-tests -Wall])
diff --git a/cosi/cositop.cc b/cosi/cositop.cc
index 975d60d6..572153ab 100644
--- a/cosi/cositop.cc
+++ b/cosi/cositop.cc
@@ -66,7 +66,7 @@ CoSiMain::CoSiMain():
 void CoSiMain::printCompileOptions() {
 	using std::cerr;
 
-	cerr << "cosi coalescent simulator, version 2.0\n\n";
+	cerr << "cosi coalescent simulator, version 2.3.0-beta.1\n\n";
 	cerr << "Compile-time options:\n";
 
 	cerr << "   COSI_SUPPORT_COALAPX (support for approximating the coalescent): " <<