Switched PhyREX from simulate to estimate mode

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,
@@ -531,7 +531,7 @@ 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
@@ -557,7 +557,7 @@ 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
@@ -575,7 +575,7 @@ 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*) \
@@ -585,7 +585,7 @@ 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

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,
@@ -296,7 +296,7 @@ AS_VAR_COPY([$1], [pkg_cv_][$1])
 AS_VAR_IF([$1], [""], [$5], [$4])dnl
 ])dnl PKG_CHECK_VAR
 
-# 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,
@@ -311,7 +311,7 @@ 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
 ])
 
@@ -327,14 +327,14 @@ 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]))])
 
 # 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,
@@ -386,7 +386,7 @@ 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,
@@ -417,7 +417,7 @@ 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,
@@ -608,7 +608,7 @@ _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,
@@ -684,7 +684,7 @@ 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,
@@ -881,7 +881,7 @@ 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,
@@ -902,7 +902,7 @@ 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,
@@ -923,7 +923,7 @@ AC_SUBST([am__leading_dot])])
 
 # 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,
@@ -973,7 +973,7 @@ 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,
@@ -1012,7 +1012,7 @@ 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,
@@ -1041,7 +1041,7 @@ 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,
@@ -1088,7 +1088,7 @@ 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,
@@ -1107,7 +1107,7 @@ 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,
@@ -1188,7 +1188,7 @@ 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,
@@ -1248,7 +1248,7 @@ 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,
@@ -1276,7 +1276,7 @@ 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,
@@ -1295,7 +1295,7 @@ 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,

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for PhyML 3.3.20180214.
+# Generated by GNU Autoconf 2.69 for PhyML 3.3.20180621.
 #
 # Report bugs to <guindon@lirmm.fr>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='PhyML'
 PACKAGE_TARNAME='phyml'
-PACKAGE_VERSION='3.3.20180214'
-PACKAGE_STRING='PhyML 3.3.20180214'
+PACKAGE_VERSION='3.3.20180621'
+PACKAGE_STRING='PhyML 3.3.20180621'
 PACKAGE_BUGREPORT='guindon@lirmm.fr'
 PACKAGE_URL=''
 
@@ -1354,7 +1354,7 @@ 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 PhyML 3.3.20180214 to adapt to many kinds of systems.
+\`configure' configures PhyML 3.3.20180621 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1425,7 +1425,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of PhyML 3.3.20180214:";;
+     short | recursive ) echo "Configuration of PhyML 3.3.20180621:";;
    esac
   cat <<\_ACEOF
 
@@ -1547,7 +1547,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-PhyML configure 3.3.20180214
+PhyML configure 3.3.20180621
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1970,7 +1970,7 @@ 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 PhyML $as_me 3.3.20180214, which was
+It was created by PhyML $as_me 3.3.20180621, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2833,7 +2833,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='phyml'
- VERSION='3.3.20180214'
+ VERSION='3.3.20180621'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2960,7 +2960,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='phyml'
- VERSION='3.3.20180214'
+ VERSION='3.3.20180621'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -6264,7 +6264,7 @@ 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 PhyML $as_me 3.3.20180214, which was
+This file was extended by PhyML $as_me 3.3.20180621, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -6330,7 +6330,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-PhyML config.status 3.3.20180214
+PhyML config.status 3.3.20180621
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

doc/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,

src/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,

src/lk.c

@@ -3216,7 +3216,7 @@ void Map_Mutations(t_node *a, t_node *d, int sa, int sd, t_edge *b, int site, in
   T = 0.0;
 #ifdef PHYTIME
   T = tree->rates->cur_l[d->num]*rr;
-#elif defined(PHYML)
+#else
   T = b->l->v*rr;
 #endif
 

src/phyrex.c

@@ -21,8 +21,8 @@ the GNU public licence. See http://www.opensource.org for details.
 
 int PHYREX_Main(int argc, char *argv[])
 {
-  /* return(PHYREX_Main_Estimate(argc,argv)); */
-  return(PHYREX_Main_Simulate(argc,argv));
+  return(PHYREX_Main_Estimate(argc,argv));
+  /* return(PHYREX_Main_Simulate(argc,argv)); */
 }
 
 //////////////////////////////////////////////////////////////
@@ -123,7 +123,7 @@ int PHYREX_Main_Estimate(int argc, char *argv[])
 
   PHYREX_Tree_Height(tree);
 
-  /* res = PHYREX_MCMC(tree); */
+  res = PHYREX_MCMC(tree);
 
   Free(res);