.gitignore

+# Generated on OS X sometimes (by dsymutil when using valgrind)
+*.dSYM
+
+# Distribution file (generated by "make distcheck" and "make dist")
+mrbayes-*.tar.gz
+
+# GNU autotools generated files
+Makefile
+autom4te.cache
+config.cache
+config.h
+config.log
+config.status
+
+# Generated by Unix build
+*~
+src/*.o
+src/.deps
+src/mb
+src/stamp-h1
+
+# hidden files
+.gitignore
+
+# OS X files
+.DS_Store
+Thumbs.db
+
+# LaTeX temporary files
+.texpadtmp
+
+# XCode project
+*.xcodeproj
+
+# Tags files
+TAGS
+tags
+
+# cscope output
+cscope.out
+
+# private file
+local.env

INSTALL

+MrBayes 3.2.7-dev (development not-yet-3.2.7 version)
+========================================================================
+
+Building MrBayes using the supplied "configure" script:
+------------------------------------------------------------------------
+
+The code in the MrBayes Git repository comes with a standard GNU
+"configure" script.  On any Unix system, these are the steps required to
+compile and optionally install MrBayes:
+
+* Run "configure" in the top-level directory to create "Makefile" (see
+  "./configure --help" for info about enabling and disabling features of
+  MrBayes, or how to install in non-standard locations etc., and also
+  read further down in this document):
+
+        $ ./configure
+
+* Make (i.e. compile) the project:
+
+        $ make
+
+  Note that if "pdflatex" or "bibtex" could not be found by the
+  "configure" script, the PDF documentation in doc/manual and
+  doc/tutorial will not be rebuilt, even if the PDF documents are
+  outdated or missing.
+
+* Install it on the system (optional).  This will install
+  the executable "mb" in /usr/local/bin, the documentation
+  in /usr/local/share/doc/mrbayes, and the example files in
+  /usr/local/share/examples/mrbayes unless the default installation
+  prefix ("/usr/local") is changed with the "--prefix" option when
+  running "configure".
+
+        $ make install
+
+To build a statically linked version of MrBayes, set the environment
+variable LDFLAGS to "-static" when configuring:
+
+    $ env LDFLAGS=-static ./configure
+
+
+Building MrBayes using the GNU autotools (Autoconf and Automake):
+------------------------------------------------------------------------
+
+MrBayes uses the GNU autotools, i.e. Automake and Autoconf, for its
+configuration and build system.  To tinker with "configure.ac" and
+"Makefile.am" and then to regenerate the "configure" script and
+associated files, there are some prerequisites that need to be in place:
+
+* Make sure Automake 1.15 (http://www.gnu.org/software/automake/)
+  is installed.
+
+* Make sure Autoconf 2.69 (http://www.gnu.org/software/autoconf/)
+  is installed.
+
+The "configure.ac" script here uses the "pkg-config" tool for detection
+of external libraries (Beagle) and also uses m4 macros from the
+autoconf-archive collection for detection of MPI, Readline, and some
+architecture-dependent compiler flags.  Therefore,
+
+* Make sure pkg-config (https://www.freedesktop.org/wiki/Software/pkg-config/)
+  is installed.
+
+* Make sure autoconf-archive 2016.03.20 (or later)
+  (http://www.gnu.org/software/autoconf-archive/) is installed.
+
+* On some systems that uses metaauto for wrapping multiple versions of
+  the GNU autotools (OpenBSD for example):
+
+        $ export AUTOCONF_VERSION=2.69
+        $ export AUTOMAKE_VERSION=1.15
+
+* On Ubuntu Linux, installing the following packages installs all of the
+  above prerequisites:
+
+    1. automake
+    2. autoconf
+    3. pkg-config
+    4. autoconf-archive
+
+  These may be installed through
+
+    sudo apt-get install automake autoconf pkg-config autoconf-archive
+
+When all the prerequisites are in place:
+
+* Run "autoreconf" to generate the "configure" script:
+
+        $ autoreconf -i
+
+* Then continue as outlined earlier in this document.
+
+
+Disabling the SSE, AVX and FMA code paths
+------------------------------------------------------------------------
+
+MrBayes will use SSE, AVX and FMA instructions to speed up computations
+on CPUs that support these instruction sets, if the compiler supports
+it.  These code paths are however optional, and if you suspect a bug in
+part of this code, you may use "--disable-sse", "--disable-avx" and/or
+"--disable-fma" to disable it when running the "configure" script.
+
+Note however, that disabling SSE will also disable AVX and FMA, and
+disabling AVX will also disable FMA.
+
+Note also that disabling these accelerated code paths will not remove
+the "-msse" (etc.) compiler flags.  These compiler flags affects what
+instructions the compiler is allowed to generate, not what code path is
+choosen for compilation.
+
+
+Picking up the Beagle library:
+------------------------------------------------------------------------
+
+Assuming Beagle (https://github.com/beagle-dev/beagle-lib) was compiled
+and installed in a standard location, it will be picked up by the
+"configure" script automatically.  If it isn't found, or the "configure"
+script is run with "--without-beagle", Beagle will not be used.
+
+If Beagle is installed in a non-default location, there are three ways
+of telling the "configure" script how to find it:
+
+1.  Use the flag "--with-beagle=PATH" where "PATH" is the prefix path
+    where the Beagle headers and libraries may be found.  For example
+    "$HOME/local", "/opt" etc.  The paths "/usr/local" and "/usr" are
+    tested if no path is specified.
+
+2.  Point the "PKG_CONFIG_PATH" environment variable to the "pkgconfig"
+    directory that Beagle installed its "hmsbeagle-1.pc" file into.
+    This file is installed if Beagle was compiled from sources, and
+    may be found in the installation's "lib" directory.  The detection
+    of Beagle will fall back on using "pkg-config" which picks up this
+    file.
+
+3.  As a last resort, it's also possible to set the "BEAGLE_CFLAGS" and
+    "BEAGLE_LIBS" environment variables prior to running "configure":
+
+    $ env BEAGLE_CFLAGS="-I$HOME/local/include/hmsbeagle-1" \
+          BEAGLE_LIBS="-L$HOME/local/lib -lhmsbeagle" \
+          ./configure
+
+
+Picking up and using MPI:
+------------------------------------------------------------------------
+
+The "configure" script will find any available MPI C compiler or
+compiler wrapper and use it (for example the one provided by OpenMPI
+(https://www.open-mpi.org/) or MPICH (https://www.mpich.org/)) if
+the "--with-mpi" flag is used.  If this flag is not used, or if
+"--without-mpi" is used, MrBayes will be compiled without support for
+MPI parallelization.
+
+You may set the "MPICC" environment variable to the name or path of a
+specific MPI C compiler, if you have many to choose from:
+
+    $ env MPICC="/usr/local/bin/mpicc" ./configure --with-mpi
+
+
+About support for the GNU Readline library:
+------------------------------------------------------------------------
+
+MrBayes will be compiled with support for the GNU Readline Library
+(https://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) (which
+allows for command line history within an interactive session, and
+command completion through pressing the "tab" key) if the Readline
+library and its associated header files are available.  However, it
+seems as if the Readline library doesn't work well together with common
+MPI implementations (OpenMPI (https://www.open-mpi.org/) and MPICH
+(https://www.mpich.org/)), so if MrBayes is configured with support for
+MPI parallelization, Readline support will be automatically disabled.
+
+A possible workaround is to use a "Readline wrapper", such as "rlwrap"
+(https://github.com/hanslub42/rlwrap), which gives you persistent
+command line history between sessions, but no command tab-completion.
+To use rlwrap with an MPI-enabled MrBayes, simply start MrBayes like
+this:
+
+    $ rlwrap mb
+
+
+# vim: filetype=text

Makefile.am

+EXTRA_DIST=	COPYING INSTALL README NEWS
+
+SUBDIRS=	src doc examples

README

+Hi,
+
+This is the GitHub repository for MrBayes, a program used for Bayesian
+inference of phylogeny.
+
+
+Build instructions, very very short version:
+
+    1. Clone the Git repository.
+    2. Refer to the document called "INSTALL" for further information.
+
+
+Current repository directory layout:
+
+    .
+    ├ doc
+    │   ├ manual                : The manual
+    │   └ tutorial              : A tutorial
+    ├ examples                  : Example input data sets
+    └ src                       : C source code
+
+
+We are currently in the process of moving everything over from
+Subversion to Git, and from SourceForge to GitHub.  The code, web
+pages and PDF manuals are already available here, and the bug tracking
+database and mailing list are very nearly sorted too.  Also, the MrBayes
+home page link at http://mrbayes.net/ is still pointing to the old web
+pages.
+
+    The new web site is available at
+
+        http://NBISweden.github.io/MrBayes/
+
+
+Historical releases are tagged with "v3.2.0" (etc.) from release 3.2.0
+onwards.
+
+The 'master' branch contains releases.
+
+The 'develop' branch should hopefully, at all times, contain working
+development code that at least compiles.  Apart from simple fixes, new
+development happens on feature branches off the 'develop' branch, and
+are merged back into 'develop' when finished.  This more or less follows
+the "git-flow" branching model.
+
+The orphaned 'gh-pages' branch contains the web site (only).
+
+After release 3.2.6 (November 2015), MrBayes entered "maintenance mode",
+and its care has been passed over to NBIS (National Bioinformatics
+Infrastructure Sweden, http://nbis.se/).  The original development
+team is still involved with the program, but any future releases will
+probably be geared more towards bug-fixes rather than addition of new
+features.
+
+With kind regards,
+    Andreas (Kusalananda) Kähäri
+    NBIS

TODO

+TODO:
+
+* Data parallelization
+
+    MrBayes currently uses MPI to run different chains in parallel
+    on different processors.  However, data sets are becoming a lot
+    larger now with respect to number of sites, so it is becoming
+    important also to distribute likelihood computations on data across
+    processors.  This would require some programming but it is not a
+    huge challenge.
+
+* Native AVX and FMA code
+
+    I have added native AVX and FMA code for the 4by4 nucleotide models.
+    It would be straightforward to add native AVX and FMA code for the
+    other models.  Particularly the AA-model would probably benefit from
+    this code (when not using the beagle library).
+
+* Dynamic scaling
+
+    Scaling of likelihoods take a surprisingly large amount of time when
+    using the standard 4by4 nucleotide models.  Maxim added dynamic
+    scaling code for the Beagle implementation but not for the native
+    likelihoood calculators, which are faster.  The dynamic scaling
+    code adjusts the rescaling frequency so that you do not rescale
+    likelihoods more often than needed to avoid numerical exceptions and
+    achieve a reasonable level of precision.  For typical-size trees
+    and the 4by4 model, no rescaling is often needed.  I added the
+    infrastructure needed to support dynamic scaling for both Beagle and
+    native calculators in December 2015.  In principle, it should be
+    straightforward now to rewrite Maxim's dynamic scaling code (which
+    is not so pretty C code) so that it works for both Beagle and native
+    likelihood calculators.

build/compile

+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2012-10-14.11; # UTC
+
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+nl='
+'
+
+# We need space, tab and new line, in precisely that order.  Quoting is
+# there to prevent tools from complaining about whitespace usage.
+IFS=" ""	$nl"
+
+file_conv=
+
+# func_file_conv build_file lazy
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts. If the determined conversion
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+  file=$1
+  case $file in
+    / | /[!/]*) # absolute file, and not a UNC file
+      if test -z "$file_conv"; then
+	# lazily determine how to convert abs files
+	case `uname -s` in
+	  MINGW*)
+	    file_conv=mingw
+	    ;;
+	  CYGWIN*)
+	    file_conv=cygwin
+	    ;;
+	  *)
+	    file_conv=wine
+	    ;;
+	esac
+      fi
+      case $file_conv/,$2, in
+	*,$file_conv,*)
+	  ;;
+	mingw/*)
+	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+	  ;;
+	cygwin/*)
+	  file=`cygpath -m "$file" || echo "$file"`
+	  ;;
+	wine/*)
+	  file=`winepath -w "$file" || echo "$file"`
+	  ;;
+      esac
+      ;;
+  esac
+}
+
+# func_cl_dashL linkdir
+# Make cl look for libraries in LINKDIR
+func_cl_dashL ()
+{
+  func_file_conv "$1"
+  if test -z "$lib_path"; then
+    lib_path=$file
+  else
+    lib_path="$lib_path;$file"
+  fi
+  linker_opts="$linker_opts -LIBPATH:$file"
+}
+
+# func_cl_dashl library
+# Do a library search-path lookup for cl
+func_cl_dashl ()
+{
+  lib=$1
+  found=no
+  save_IFS=$IFS
+  IFS=';'
+  for dir in $lib_path $LIB
+  do
+    IFS=$save_IFS
+    if $shared && test -f "$dir/$lib.dll.lib"; then
+      found=yes
+      lib=$dir/$lib.dll.lib
+      break
+    fi
+    if test -f "$dir/$lib.lib"; then
+      found=yes
+      lib=$dir/$lib.lib
+      break
+    fi
+    if test -f "$dir/lib$lib.a"; then
+      found=yes
+      lib=$dir/lib$lib.a
+      break
+    fi
+  done
+  IFS=$save_IFS
+
+  if test "$found" != yes; then
+    lib=$lib.lib
+  fi
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+  # Assume a capable shell
+  lib_path=
+  shared=:
+  linker_opts=
+  for arg
+  do
+    if test -n "$eat"; then
+      eat=
+    else
+      case $1 in
+	-o)
+	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
+	  eat=1
+	  case $2 in
+	    *.o | *.[oO][bB][jJ])
+	      func_file_conv "$2"
+	      set x "$@" -Fo"$file"
+	      shift
+	      ;;
+	    *)
+	      func_file_conv "$2"
+	      set x "$@" -Fe"$file"
+	      shift
+	      ;;
+	  esac
+	  ;;
+	-I)
+	  eat=1
+	  func_file_conv "$2" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-I*)
+	  func_file_conv "${1#-I}" mingw
+	  set x "$@" -I"$file"
+	  shift
+	  ;;
+	-l)
+	  eat=1
+	  func_cl_dashl "$2"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-l*)
+	  func_cl_dashl "${1#-l}"
+	  set x "$@" "$lib"
+	  shift
+	  ;;
+	-L)
+	  eat=1
+	  func_cl_dashL "$2"
+	  ;;
+	-L*)
+	  func_cl_dashL "${1#-L}"
+	  ;;
+	-static)
+	  shared=false
+	  ;;
+	-Wl,*)
+	  arg=${1#-Wl,}
+	  save_ifs="$IFS"; IFS=','
+	  for flag in $arg; do
+	    IFS="$save_ifs"
+	    linker_opts="$linker_opts $flag"
+	  done
+	  IFS="$save_ifs"
+	  ;;
+	-Xlinker)
+	  eat=1
+	  linker_opts="$linker_opts $2"
+	  ;;
+	-*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+	  func_file_conv "$1"
+	  set x "$@" -Tp"$file"
+	  shift
+	  ;;
+	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+	  func_file_conv "$1" mingw
+	  set x "$@" "$file"
+	  shift
+	  ;;
+	*)
+	  set x "$@" "$1"
+	  shift
+	  ;;
+      esac
+    fi
+    shift
+  done
+  if test -n "$linker_opts"; then
+    linker_opts="-link$linker_opts"
+  fi
+  exec "$@" $linker_opts
+  exit 1
+}
+
+eat=
+
+case $1 in
+  '')
+     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file 'INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+    func_cl_wrapper "$@"      # Doesn't return...
+    ;;
+esac
+
+ofile=
+cfile=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as 'compile cc -o foo foo.c'.
+	# So we strip '-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no '-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # '.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

src/install-sh → build/install-sh

 #!/bin/sh
 #
+# $NetBSD: install-sh.in,v 1.6 2012/01/11 13:07:31 hans Exp $
+# This script now also installs multiple files, but might choke on installing
+# multiple files with spaces in the file names.
+#
 # install - install a program, script, or datafile
-# This comes from X11R5.
+# This comes from X11R5 (mit/util/scripts/install.sh).
+#
+# Copyright 1991 by the Massachusetts Institute of Technology
+#
+# Permission to use, copy, modify, distribute, and sell this software and its
+# documentation for any purpose is hereby granted without fee, provided that
+# the above copyright notice appear in all copies and that both that
+# copyright notice and this permission notice appear in supporting
+# documentation, and that the name of M.I.T. not be used in advertising or
+# publicity pertaining to distribution of the software without specific,
+# written prior permission.  M.I.T. makes no representations about the
+# suitability of this software for any purpose.  It is provided "as is"
+# without express or implied warranty.
 #
 # Calling this script install-sh is preferred over install.sh, to prevent
 # `make' implicit rules from creating a file called install from it
@@ -9,8 +25,6 @@
 #
 # This script is compatible with the BSD install script, but was written
 # from scratch.
-#
-
 
 # set DOITPROG to echo to test this script
 
@@ -20,6 +34,7 @@ doit="${DOITPROG-}"
 
 # put in absolute paths if you don't have them in your path; or use env. vars.
 
+awkprog="${AWKPROG-awk}"
 mvprog="${MVPROG-mv}"
 cpprog="${CPPROG-cp}"
 chmodprog="${CHMODPROG-chmod}"
@@ -29,21 +44,34 @@ stripprog="${STRIPPROG-strip}"
 rmprog="${RMPROG-rm}"
 mkdirprog="${MKDIRPROG-mkdir}"
 
-tranformbasename=""
-transform_arg=""
-instcmd="$mvprog"
-chmodcmd="$chmodprog 0755"
+instcmd="$cpprog"
+instflags=""
+pathcompchmodcmd="$chmodprog 755"
+chmodcmd="$chmodprog 755"
 chowncmd=""
 chgrpcmd=""
 stripcmd=""
+stripflags=""
 rmcmd="$rmprog -f"
 mvcmd="$mvprog"
 src=""
+msrc=""
 dst=""
 dir_arg=""
+suffix=""
+suffixfmt=""
 
 while [ x"$1" != x ]; do
     case $1 in
+	-b) suffix=".old"
+	    shift
+	    continue;;
+
+	-B) suffixfmt="$2"
+	    shift
+	    shift
+	    continue;;
+
 	-c) instcmd="$cpprog"
 	    shift
 	    continue;;
@@ -57,6 +85,11 @@ while [ x"$1" != x ]; do
 	    shift
 	    continue;;
 
+	-m*)
+	    chmodcmd="$chmodprog ${1#-m}"
+	    shift
+	    continue;;
+
 	-o) chowncmd="$chownprog $2"
 	    shift
 	    shift
@@ -71,87 +104,98 @@ while [ x"$1" != x ]; do
 	    shift
 	    continue;;
 
-	-t=*) transformarg=`echo $1 | sed 's/-t=//'`
+	-S) stripcmd="$stripprog"
+	    stripflags="-S $2 $stripflags"
+	    shift
 	    shift
 	    continue;;
 
-	-b=*) transformbasename=`echo $1 | sed 's/-b=//'`
+	-p) instflags="-p"
 	    shift
 	    continue;;
 
-	*)  if [ x"$src" = x ]
+	*)  if [ x"$msrc" = x ]
 	    then
-		src=$1
+		msrc="$dst"
 	    else
-		# this colon is to work around a 386BSD /bin/sh bug
-		:
-		dst=$1
+		msrc="$msrc $dst"
 	    fi
+	    src="$dst"
+	    dst="$1"
 	    shift
 	    continue;;
     esac
 done
 
-if [ x"$src" = x ]
+if [ x"$dir_arg" = x ]
+then
+	dstisfile=""
+	if [ ! -d "$dst" ]
 	then
-	echo "install:	no input file specified"
+		if [ x"$msrc" = x"$src" ]
+		then
+			dstisfile=true
+		else
+			echo "install: destination is not a directory"
 			exit 1
+		fi
+	fi
 else
-	true
+	msrc="$msrc $dst"
 fi
 
+if [ x"$msrc" = x ]
+then
+	echo "install: no destination specified"
+	exit 1
+fi      
+
+for srcarg in $msrc; do
+
 if [ x"$dir_arg" != x ]; then
-	dst=$src
-	src=""
 
-	if [ -d $dst ]; then
-		instcmd=:
-	else
-		instcmd=mkdir
-	fi
+	dstarg="$srcarg"
 else
+	dstarg="$dst"
 
-# Waiting for this to be detected by the "$instcmd $src $dsttmp" command
+# Waiting for this to be detected by the "$instcmd $srcarg $dsttmp" command
 # might cause directories to be created, which would be especially bad 
 # if $src (and thus $dsttmp) contains '*'.
 
-	if [ -f $src -o -d $src ]
+	if [ -f "$srcarg" ]
 	then
-		true
-	else
-		echo "install:  $src does not exist"
-		exit 1
-	fi
-	
-	if [ x"$dst" = x ]
+		doinst="$instcmd $instflags"
+	elif [ -d "$srcarg" ]
 	then
-		echo "install:	no destination specified"
+		echo "install: $srcarg: not a regular file"
 		exit 1
+	elif [ "$srcarg" = "/dev/null" ]
+	then
+		doinst="$cpprog"
 	else
-		true
+		echo "install:  $srcarg does not exist"
+		exit 1
 	fi
 	
 # If destination is a directory, append the input filename; if your system
 # does not like double slashes in filenames, you may need to add some logic
 
-	if [ -d $dst ]
+	if [ -d "$dstarg" ]
 	then
-		dst="$dst"/`basename $src`
-	else
-		true
+		dstarg="$dstarg"/`basename "$srcarg"`
 	fi
 fi
 
 ## this sed command emulates the dirname command
-dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
+dstdir=`echo "$dstarg" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
 
 # Make sure that the destination directory exists.
 #  this part is taken from Noah Friedman's mkinstalldirs script
 
 # Skip lots of stat calls in the usual case.
 if [ ! -d "$dstdir" ]; then
-defaultIFS=''
-
+defaultIFS='	
+'
 IFS="${IFS-${defaultIFS}}"
 
 oIFS="${IFS}"
@@ -168,7 +212,11 @@ while [ $# -ne 0 ] ; do
 
 	if [ ! -d "${pathcomp}" ] ;
         then
-		$mkdirprog "${pathcomp}"
+		$doit $mkdirprog "${pathcomp}"
+        	if [ x"$chowncmd" != x ]; then $doit $chowncmd "${pathcomp}"; else true ; fi &&
+        	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd "${pathcomp}"; else true ; fi &&
+        	if [ x"$pathcompchmodcmd" != x ]; then $doit $pathcompchmodcmd "${pathcomp}"; else true ; fi
+
 	else
 		true
 	fi
@@ -179,40 +227,49 @@ fi
 
 	if [ x"$dir_arg" != x ]
 	then
-	$doit $instcmd $dst &&
-
-	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi &&
-	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi &&
-	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi &&
-	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi
+		if [ -d "$dstarg" ]; then
+			true
 		else
+			$doit $mkdirprog "$dstarg" &&
 
-# If we're going to rename the final executable, determine the name now.
-
-	if [ x"$transformarg" = x ] 
-	then
-		dstfile=`basename $dst`
-	else
-		dstfile=`basename $dst $transformbasename | 
-			sed $transformarg`$transformbasename
+			if [ x"$chowncmd" != x ]; then $doit $chowncmd "$dstarg"; else true ; fi &&
+			if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd "$dstarg"; else true ; fi &&
+			if [ x"$chmodcmd" != x ]; then $doit $chmodcmd "$dstarg"; else true ; fi
 		fi
+	else
 
-# don't allow the sed command to completely eliminate the filename
-
-	if [ x"$dstfile" = x ] 
+		if [ x"$dstisfile" = x ]
 		then
-		dstfile=`basename $dst`
+			file=$srcarg
 		else
-		true
+			file=$dst
 		fi
 
+		dstfile=`basename "$file"`
+		dstfinal="$dstdir/$dstfile"
+
 # Make a temp file name in the proper directory.
 
 		dsttmp=$dstdir/#inst.$$#
 
+# Make a backup file name in the proper directory.
+		case x$suffixfmt in
+		*%*)	suffix=`echo x |
+			$awkprog -v bname="$dstfinal" -v fmt="$suffixfmt" '
+			{ cnt = 0;
+			  do {
+				sfx = sprintf(fmt, cnt++);
+				name = bname sfx;
+			  } while (system("test -f " name) == 0);
+			  print sfx; }' -`;;
+		x)	;;
+		*)	suffix="$suffixfmt";;
+		esac
+		dstbackup="$dstfinal$suffix"
+
 # Move or copy the file name to the temp name
 
-	$doit $instcmd $src $dsttmp &&
+		$doit $doinst $srcarg "$dsttmp" &&
 
 		trap "rm -f ${dsttmp}" 0 &&
 
@@ -222,17 +279,23 @@ else
 # ignore errors from any of these, just make sure not to ignore
 # errors from the above "$doit $instcmd $src $dsttmp" command.
 
-	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi &&
-	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi &&
-	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi &&
-	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi &&
+		if [ x"$chowncmd" != x ]; then $doit $chowncmd "$dsttmp"; else true;fi &&
+		if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd "$dsttmp"; else true;fi &&
+		if [ x"$stripcmd" != x ]; then $doit $stripcmd $stripflags "$dsttmp"; else true;fi &&
+		if [ x"$chmodcmd" != x ]; then $doit $chmodcmd "$dsttmp"; else true;fi &&
 
 # Now rename the file to the real destination.
 
-	$doit $rmcmd -f $dstdir/$dstfile &&
-	$doit $mvcmd $dsttmp $dstdir/$dstfile 
-
+		if [ x"$suffix" != x ] && [ -f "$dstfinal" ]
+		then
+			$doit $mvcmd "$dstfinal" "$dstbackup"
+		else
+			$doit $rmcmd -f "$dstfinal"
 		fi &&
+		$doit $mvcmd "$dsttmp" "$dstfinal"
+	fi
+
+done &&
 
 
 exit 0

debian/changelog

-mrbayes (3.2.6+dfsg-3) UNRELEASED; urgency=medium
+mrbayes (3.2.7~pre-1) UNRELEASED; urgency=medium
 
+  * New upstream version
   * Upstream moved to Github
-
- -- Andreas Tille <tille@debian.org>  Fri, 16 Feb 2018 09:46:59 +0100
+  * hardening=+all
+  * Point Vcs fields to Salsa
+  * Standards-Version: 4.1.4
+  * debhelper 11
+  * Drop inactive maintainers from Uploaders
+  * No Priority=extra for doc package
+  * Do not include rpath
+
+ -- Andreas Tille <tille@debian.org>  Wed, 27 Jun 2018 08:45:36 +0200
 
 mrbayes (3.2.6+dfsg-2) unstable; urgency=medium
 

debian/compat

-9
+11

debian/control

 Source: mrbayes
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Fernando Ribeiro <fernando@staff.nerdgroup.org>,
-           Steffen Moeller <moeller@debian.org>,
-           Dominique Belhachemi <domibel@debian.org>,
-           Pjotr Prins <pjotr.debian@thebird.nl>,
+Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                libreadline-dev,
                mpi-default-dev,
                libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2),
                autoconf,
                automake
-Standards-Version: 4.0.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mrbayes.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/mrbayes.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/mrbayes
+Vcs-Git: https://salsa.debian.org/med-team/mrbayes.git
 Homepage: http://mrbayes.csit.fsu.edu/
 
 Package: mrbayes
@@ -54,7 +51,6 @@ Description: Bayesian Inference of Phylogeny - mpi version
 Package: mrbayes-doc
 Architecture: all
 Section: doc
-Priority: extra
 Depends: ${misc:Depends}
 Enhances: mrbayes
 Description: Bayesian Inference of Phylogeny - manual