Commit 5bdcbce1 authored by Andreas Tille's avatar Andreas Tille

New upstream version 5.2

parent a42bb34d
since 1999 by Heiko A. Schmidt, Korbinian Strimmer,
Martin Vingron, Arndt von Haeseler
1995-1999 by Korbinian Strimmer and Arndt von Haeseler
($Id$)
Heiko A. Schmidt
MPI for Molecular Genetics
Computational Molecular Biology
Ihnestrasse 73
D-14195 Berlin
Germany
email: hschmidt@molgen.mpg.de,
http://cmb.molgen.mpg.de
Korbinian Strimmer
Department of Statistics
University of Munich
Ludwigstrasse 33
D-80539 Munich
Germany
email: strimmer@stat.uni-muenchen.de
http://www.stat.uni-muenchen.de/~strimmer/
Martin Vingron
MPI for Molecular Genetics
Computational Molecular Biology
Ihnestrasse 73
D-14195 Berlin
Germany
email: vingron@molgen.mpg.de,
http://cmb.molgen.mpg.de
Arndt von Haeseler
HHU Duesseldorf
Mathematisches Institut
Abteilung fuer Informatik
Universitaetsstr. 1
D-40225 Duesseldorf
Germany
email: haeseler@cs.uni-duesseldorf.de
http://www.cs.uni-duesseldorf.de/~haeseler/
and
John-von-Neumann Institut fuer Computing
Forschungsgruppe Bioinformatik
FZ-Juelich
D-52425 Juelich
Germany
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Copyright 1994, 1995, 1996, 1999, 2000, 2001 Free Software Foundation,
Inc.
This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.
Basic Installation
==================
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It can also use an optional file (typically called `config.cache'
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If you need to do unusual things to compile the package, please try
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The simplest way to compile this package is:
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Running `configure' takes awhile. While running, it prints some
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====================================
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Installation Names
==================
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================
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==================
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======================
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#
# Makefile.am
#
#
# Part of TREE-PUZZLE 5.2 (July 2004)
#
# (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
# (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer,
# M. Vingron, and Arndt von Haeseler
# (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
#
# All parts of the source except where indicated are distributed under
# the GNU public licence. See http://www.opensource.org for details.
#
# ($Id$)
#
EXTRA_DIST =
SUBDIRS = src doc data tests
This diff is collapsed.
TREE-PUZZLE 5.2
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
from molecular sequence data by maximum likelihood. It implements a
fast tree search algorithm, quartet puzzling, that allows analysis of
large data sets and automatically assigns estimations of support to each
internal branch. TREE-PUZZLE also computes pairwise maximum likelihood
distances as well as branch lengths for user specified trees. Branch
lengths can also be calculated under the clock-assumption. In addition,
TREE-PUZZLE offers a novel method, likelihood mapping, to investigate
the support of a hypothesized internal branch without computing an overall
tree and to visualize the phylogenetic content of a sequence alignment.
TREE-PUZZLE also conducts a number of statistical tests on the data set
(chi-square test for homogeneity of base composition, likelihood ratio
to test the clock hypothesis, Kishino-Hasegawa test). The models of
substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids,
and F81 for two-state data. Rate heterogeneity is modelled by a
discrete Gamma distribution and by allowing invariable sites.
The corresponding parameters can be inferred from the data set.
INSTALLATION
For compile an intall instructions see INSTALL and doc/manual.html
In most cases on UNIX machines the following should work
(if the prefix is left out configure the executable are installed
in /urs/local):
sh ./configure --prefix=/usr/local
make
make install
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dnl $Id$
dnl Disable caching.
define([AC_CACHE_LOAD], )dnl
define([AC_CACHE_SAVE], )dnl
dnl Process this file with autoconf to produce a configure script.
AC_INIT
AC_CANONICAL_BUILD
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE(tree-puzzle, 5.2)
AM_CONFIG_HEADER(src/config.h)
dnl Gets build and target system type.
dnl Checks for programs.
AC_PROG_CC
AC_PROG_CC_C_O
AC_PROG_INSTALL
AC_PROG_MAKE_SET
dnl ---------------------------------------------------------------------
dnl Test function to test whether mpicc works correctly
dnl ---------------------------------------------------------------------
AC_DEFUN(AC_TEST_MPICC,[dnl
if test "$1" != "" ; then
if test "$MPICCSET" = "" ; then
cat > conftest.c <<EOF
#include<mpi.h>
int main (int argc, char **argv)
{
MPI_Init(&argc,&argv);
MPI_Finalize();
exit(0);
}
EOF
MPICC=$1
dnl if test "$MPICC" != "$CC" ; then
dnl fi
if test "$MPICC" != "" ; then
AC_MSG_CHECKING(whether $MPICC works as MPI compiler)
$MPICC conftest.c -o conftest > /dev/null 2>&1
if test $? = 0 ; then
AC_MSG_RESULT(yes)
#MPICC=$MPICC
MPILIBS=
MPICCSET=$MPICC
PPUZZLE=ppuzzle
else
AC_MSG_RESULT(no)
AC_MSG_CHECKING(whether $MPICC needs -lmpi)
$MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1
if test $? = 0 ; then
AC_MSG_RESULT(yes)
#MPICC=$PCC
MPILIBS=-lmpi
MPICCSET=$MPICC
PPUZZLE=ppuzzle
else
AC_MSG_RESULT(no)
MPICC=
MPILIBS=
MPICCSET=
PPUZZLE=
fi
fi
fi
rm -f *.conftest*
fi
fi ])
if test "$MPICC" != "" ; then
AC_PATH_PROG(MPICC0, $MPICC)
fi
AC_PATH_PROG(MPICC1, mpcc)
AC_PATH_PROG(MPICC2, hcc)
AC_PATH_PROG(MPICC3, mpicc)
AC_PATH_PROG(MPICC4, mpicc_lam)
AC_PATH_PROG(MPICC5, mpicc_mpich)
AC_PATH_PROG(MPICC6, cc)
AC_TEST_MPICC($MPICC0)
AC_TEST_MPICC($MPICC1)
AC_TEST_MPICC($MPICC2)
AC_TEST_MPICC($MPICC3)
AC_TEST_MPICC($MPICC4)
AC_TEST_MPICC($MPICC5)
AC_TEST_MPICC($MPICC6)
ac_cv_prog_MPICC=$MPICC
dnl ---------------------------------------------------------------------
dnl Test function to test whether the compiler handles quotes correctly
dnl ---------------------------------------------------------------------
AC_DEFUN(AC_TEST_CCQUOTES,[dnl
if test "$1" != "" ; then
cat > conftest.c <<EOF
#include<stdio.h>
int main (int argc, char **argv)
{
printf ("%s-%s", PACKAGE, VERSION);
exit(0);
}
EOF
CCQ=$1
if test "$CCQ" != "" ; then
AC_MSG_CHECKING(whether $CCQ handles quotes correctly)
$CCQ -DPACKAGE=\"$PACKAGE\" -DVERSION=\"$VERSION\" conftest.c -o conftest > /dev/null 2>&1
if test $? = 0 ; then
DUMMY=`./conftest`
if test "$DUMMY" = "$PACKAGE-$VERSION" ; then
AC_MSG_RESULT(yes)
else
AC_MSG_RESULT(no)
fi
else
AC_MSG_RESULT(no)
fi
fi
mv conftest.c `basename $CCQ`.conftest.c
rm -f *.conftest*
fi ])
AC_TEST_CCQUOTES($MPICC)
AC_TEST_CCQUOTES($CC)
AC_SUBST(MPICC)
AC_SUBST(MPILIBS)
AC_SUBST(MPIDEFS)
AC_SUBST(MPICFLAGS)
AC_SUBST(PPUZZLE)
dnl Checks for libraries.
dnl Replace `main' with a function in -lm:
AC_CHECK_LIB(m, main)
dnl AC_CHECK_LIB(mpi, main)
dnl Checks for header files.
AC_HEADER_STDC
AC_CHECK_HEADERS(limits.h)
dnl AC_CHECK_HEADERS([mpi.h])
dnl AC_CHECK_HEADERS([rpc/xdr.h])
dnl Checks for typedefs, structures, and compiler characteristics.
AC_C_CONST
AC_TYPE_SIZE_T
dnl Checks for library functions.
dnl AC_CHECK_FUNCS(xdr_u_char)
dnl AC_CHECK_FUNCS(xdr_double)
dnl AC_CHECK_FUNCS(xdrstdio_create)
dnl AC_CHECK_FUNCS(xdr_destroy)
dnl AC_CHECK_FUNCS(xdr_inline)
AC_CONFIG_FILES([Makefile src/Makefile src/sprng/Makefile doc/Makefile data/Makefile tests/Makefile])
AC_OUTPUT
[tree - ((B2,(E2,C2)),(B1a,(E1a,C1a))) ]
[ lh=-18965.865869 ](EFG_MYCGE:0.35044,(((((EF1A_SULAC:0.27436,EF1A_DESMO:0.15452)98:0.06186,
EF1A_AERPE:0.19726)100:0.16339,((EF11_DAUCA:0.19788,EF1A_DICDI:0.17054)
68:0.08680,(EF11_HUMAN:0.04646,EF12_MOUSE:0.04777)64:0.06487,EF1A_CAEEL:0.12845)
88:0.47056)100:0.66538,((EFTU_ECOLI:0.16964,EFTU_HELPY:0.21648)100:0.10227,
EFTU_MYCGE:0.22380)100:0.82551)100:2.71210,(((((EF2_MOUSE:0.00532,
EF2_HUMAN:0.00411)100:0.11711,EF2_CAEEL:0.10100)98:0.13112,EF2_DICDI:0.32291)
94:0.08935,EF2_BETVU:0.22108)100:0.79422,((EF2_SULAC:0.22098,EF2_DESMO:0.26389)
100:0.06212,EF2_AERPE:0.15059)100:0.23638)99:0.48379)100:1.02287,
(EFG_ECOLI:0.28597,EFG_HELPY:0.19713)99:0.14542);
[tree2 - ((E2,(B2,C2)),(E1a,(B1a,C1a))) ]
(
(
[E+2]
(
(
(
(
EF2_HUMAN,
EF2_MOUSE
),
EF2_CAEEL
),
EF2_DICDI
),
EF2_BETVU
)
[E-2]
,
(
[B+2]
(
EFG_MYCGE,
(
EFG_ECOLI,
EFG_HELPY
)
)
[B-2]
,
[A+2]
(
EF2_AERPE,
(
EF2_DESMO,
EF2_SULAC
)
)
[A-2]
)
)
,[root]
(
[E+1a]
(
(
EF11_HUMAN,
EF12_MOUSE
),
EF1A_CAEEL,
(
EF11_DAUCA,
EF1A_DICDI
)
)
[E-1a]
,
(
[B+1a]
(
(
EFTU_ECOLI,
EFTU_HELPY
),
EFTU_MYCGE
)
[B-1a]
,
[A+1a]
(
(
EF1A_DESMO,
EF1A_SULAC
),
EF1A_AERPE
)
[A-1a]
)
)
)
;
[tree3 - ((C2,(E2,B2)),(C1a,(E1a,B1a))) ]
(
(
[A+2]
(
EF2_AERPE,
(
EF2_DESMO,
EF2_SULAC
)
)
[A-2]
,
(
[E+2]
(
(
(
(
EF2_HUMAN,
EF2_MOUSE
),
EF2_CAEEL
),
EF2_DICDI
),
EF2_BETVU
)
[E-2]
,
[B+2]
(
EFG_MYCGE,
(
EFG_ECOLI,
EFG_HELPY
)
)
[B-2]
)
),
[root]
(
[A+1a]
(
(
EF1A_DESMO,
EF1A_SULAC
),
EF1A_AERPE
)
[A-1a]
,
(
[E+1a]
(
(
EF11_HUMAN,
EF12_MOUSE
),
EF1A_CAEEL,
(
EF11_DAUCA,
EF1A_DICDI
)
)
[E-1a]
,
[B+1a]
(
(
EFTU_ECOLI,
EFTU_HELPY
),
EFTU_MYCGE
)
[B-1a]
)
)
)
;
This diff is collapsed.
#
# Makefile.am
#
#
# Part of TREE-PUZZLE 5.2 (July 2004)
#
# (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
# (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer,
# M. Vingron, and Arndt von Haeseler