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......@@ -5,18 +5,246 @@ ChangeLog
Version date what has been changed
TODO:
missing quartet handling
missing quartet counting in parallel case
- positive 'penalties' for the non-penalized subtree
- missing quartet handling
- missing quartet counting in parallel case
- primes-lcg64.c: int offset <=> unsigned MAXPRIMEOFFSET ??? (HAS)
- user defined substitution matrices
- more protein substitution matrices (cf. MrBayes)
- AA models: Poisson, Equalin, mtMAM, rtREV, cpREV, BLOSUM, GTR, LG
(Jones, Dayhoff, mtREV, WAG, VT exist already)
- SeqFault by -wsl auf consensus
- branchlength correction for ML evaluation of rooted usertrees
(currently one of the two branchlengths at the root is lost
when the root bifurcation is removed)
- lcg64 -> mlfg (done?!?)
- SPRNG for the sequential run (cmdline: number of runs/current
number/seed), if parallel run are run sequentially
- CHECK: continuous *.ptall file for parallel version
- split rate-heterogeneity block in *.puzzle file
order: rate-heterogeneity parameters, quartet statistic, site
specific rate categories
- check MP-, ME-, NJ-quartet code
- quartet distances for trees: 2 trees (branch lengths=1) ->
2 matrices -> quart-topol easy to compute.
- column aliasing on quartet level to speed up likelihood calculation
- fix mem leakage in SPRNG (init)
- implement '-m100', '-m50', '-mrel', '-mlrel', '-mext'
'-m100' include Si, if P(Si) == 100%
'-m50' include Si, if P(Si) > 50% [default]
'-mrel' include Si, if Si congruent to all Sj (j<i), else stop (done)
'-mlrel' include Si, if Si congruent to all Sj (j<i)
'-mext' include Si, if Si congruent to all Sj in current Tree
- check EPS creation in clustered likelihood mapping (done, SVG implemented)
- check for output of additional top string on likelihood mapping
triangle
- commandline option to increase CHAR_PER_TREENODE
DONE:
5.2 14.07.2004 - Version 5.2 !!!
5.3.rc16 05.12.2014 - sliding windows informative sites output in VisRec
format implemented
- use compiler switch USE_RECDETEC in puzzle.h to
switch between RecDetec and VisRec format
- implemented -statsonly flag to stop after alignment
statistics
- removed a few debug outputs
5.3.rc15 26.05.2014 - clean up of a number of compiler warnings
5.3.rc14 04.10.2013 - informative site counts added
5.3.rc13 13.08.2013 - informative sites (now correct double casts)
5.3.rc12 26.06.2013 - LG model added
5.3.rc11 27.02.2013 - autotools files updated
- options -prefix= and -param= fixed for paths
with space characters
5.3.rc10 03.01.2013 - nasty realloc error fixed, led to occasional
crashes in the realloc of myrealloc due to data
corruption
- some debug messages removed or commented out
5.3.rc9 17.08.2012 - output of the number of nt/aa-pairs of two seqs
in tstv output
- writing aliinfo file behind savealiinfo_optn
check (was writing almost empty file before)
- some debug messages commented out
20.08.2012 - edit dist added to tstv output
- a few compiler switches added to lcg64.c to
prevent compile-time warnings
5.3.rc8 20.01.2012 - aliinfo output
- split occurence
5.3.rc7 14.07.2010 - Increased CHAR_PER_TREENODE in ml2.c from 53 to 64.
5.3.rc6 30.09.2009 - informative site evaluation extended: count and output
also variable but uninformative and fully informative site;
discarded all taxon-wise informative counting except
informative and uninformative (all others are equal to
that of the alignment.
- corrections in SVG: colors added; stroke removed in
circles (too large due to the stroke line);
coordinates corrected in plotlmpointcolor (x1000)
5.3.rc5 28.09.2009 - computation of pairwise edit distances (incl. gaps+
ambiguous chars as separate state / excl. sites
with gaps or amiguous characters) and out put
to *.editdist file (flag '-weditdist')
- output format of *.rdstats streamlined
- corrections in the help/usage output
29.09.2009 - ChangeLog file and TODOs checked and updated
- exit character 'q' in cluster selection for
likelihood mapping to get back to menu.
5.3.rc4 14.09.2009 - hint at ts/tv parameter input: "0.5 for JC69/F81"
22.09.2009 - evaluation of parsimony informative sites of
the of alignment summary and per sequence
- output to RecDetec stats file (-wrdsf: *.rdstats)
5.3.rc3 13.09.2009 - SVG code corrected:
- using rotate instead on transform in rectangles,
- using text-anchor="middle" to center,
- order of x and y coordinates exchanged,
- output of corner labels of upper triangle
5.3.rc2 30.08.2009 - SVG code scaled up from 0-1 to 0-1000
5.3.rc1 29.08.2008 - command line parameter, if click-started
- little bug fix in KH-test if tree are equal
- SVG output of likelihood mapping
- outgroup option added for consensus
CODE FREEZE for 5.3
===================
5.2.pl21 11.04.2008 - file pointer error fixed (writing final check double)
5.2.pl20 07.04.2008 - check double added before and after binary block in
binary quartet likelihood and quartet files
10.04.2008 - debug messages eliminated with compiler switch
BININPUTDEBUG
5.2.pl19 26.03.2008 - bus error bug fixed, for -wsl bei consensus
- plain split output added
5.2.pl18 20.10.2007 - site character frequencies output to *.sitefreqs
07.02.2008 - general substitution counts output to *.tstv
for visualization with R, not only TS:TV
- several cmdline options added to "-h" help.
- default # of Gamma rates numcats = 4 (8 before).
5.2.pl17 18.10.2007 - output of character frequencies per site added
currently to output.sitefreqs (for visualization with R)
20.10.2007 - superqp fixes added
- re-read of names via *.subsetmat file corrected
- consistency check *.subsetmat file added
- handling of quartet info 15=(1111) for missing data
5.2.pl16 05.06.2007 - ts:tv data output added for visualization with R
5.2.pl15 27.09.2006 - quarted puzzling with only those quartets which
contain the root taxon.
- added: -rootstart, rootstart_optn
- added: -rootqonly, rootquartsonly_optn
5.2.pl14 11.09.2006 - tp_exit added for click-started sessions
- consensus debugged, many comments added
5.2.pl13 11.09.2006 - fix 'Unable to proceed' exits for *-click*
- memory allocation for >257 species (works on 64bit)
- output of quartet statistics sums added
- likelihood mapping: output mappings per sequence
5.2.pl12 26.11.2005 - quartet statistics output to file added
5.2.pl11 21.11.2005 - sequence-wise likelihood mapping (almost) finished
22.11.2005 - final fixes in sequence-wise likelihood mapping
5.2.pl10 14.06.2005 - changing from hard wired voting scheme to
command line controlled (-voting)
- add '-voting' to '-hhh'
5.2.pl9 11.06.2005 - all different voting schemes (penalty, bonus,
bonus-penalty) implemented for path/subtree
normalized/absolute in pstep-tripl.c
14.06.2005 - memory leakage fixed (freeing node-penalty arrays)
- weighted voting (partly =1*2 / partyl resolved =2*1)
5.2.pl8 18.03.2005 - "identical seq <- zero dist" remark outside loop fix
03.04.2005 - minedges array size: Maxspc -> Maxbrnch
- checkquartet outputs the neighbor to the addition
sequence besides the penalty neighbor
04.04.2005 - implementation of a penalty/bonus weighting method
(triplbonus)
22.04.2005 - renamed mrca.c recur.c split.c triplbonus.c to
pstep-*.c
04.05.2005 - ... fixed Makefile.am accordingly
05.06.2005 - pstep-tripl.c: triplet based subtree votings finished
(currently with test output, todo path bonus)
(switch off output: define QUIET)
(switch on output: define PSTEP_TRIPL)
5.2.pl7 02.03.2005 - output of chi-square values added (for Ross)
5.2.pl6 28.01.2005 - trees in treefile don't contain LFs
- continuous *.ptall file for parallel version
- (c)-Notices updated to 2005
01.02.2004 - MPI bug fixed, called twice MPI_Finalized
- tp_exit's fixed
5.2.pl5 21.10.2004 - RNG type output changed from stderr to stdout
27.01.2005 - new flags (mainly for parallel/batch processing)
-wallptrees - write successively all puzzling
trees to PREFIX.allquart
-param=YYY - use file 'YYY' for parameter input
(instead of stdin)
5.2.pl4 14.09.2004 - warnings fixed in SPRNG
- autotools updated (automake 1.7)
17.09.2004 - NEXUS fprintfsortedpstrees: context checking, whether
allowed
- output of MLStep+PuzStep time only when doing QP
- Output of inner branch lench added (-wqltb/-wqlta)
5.2.pl3 13.09.2004 - ME/NJ/MP quartets hidden by "QUART_TEST define"
- menu item "Approximate quartet likelihood" replaced
by "Quartet evaluation criterion"
- 'identical sequence' comment added to report
- likelihood mapping color added test-wise (COL_TEST)
14.09.2004 - comma added after last nexus split (for SplitsTree)
- distributed for GfBS 2004 workshop, Stuttgart
5.2.pl2 01.09.2004 - NEXUS output refined (distances added)
- temporariy '9' option added to menu for NEXUS
- distributed for VEME 2004 workshop, Helsinki
5.2.pl1 12.07.2004 - quartet criteria ME, MP, NJ added (MP - to be finished)
11.08.2004 - quartet criteria added to cmdline/menu
13.08.2004 - treesort.c: taxon IDs in treestring 0..n-1 -> 1..n
for NEXUS output
- 'sed' corrected to 'sed -e'; 'sed' for VERSION
corrected for empty VERSION and for the '.' -> '\.'
23.08.2004 - ml2.c: prepared for computation/output of posterior
site rate likelihood for best site rate.
Marked with 'posterior sitelhl' in the comment.
- ml2.c: output fixed of invariant rates (Rates[0 - 1])
29.08.2004 - NEXUS output (trees and splits) todo: simple files
30.08.2004 - doc/fig/Makefile deleted from configure.ac
- compiler warnings fixed
5.2 12.07.2004 - Version 5.2 !!!
NEW RELEASE
===========
5.2.rc17 14.07.2004 - Manual sources moved out of the package
- numerous changes in the manual
5.2.rc16 12.07.2004 - Makefile.am: double distclean rule removed
- fflush added before mygets() - because of Windows
- manual spell-checked
......
INSTALL 100644 → 100755
View file @ 7d894615
Copyright 1994, 1995, 1996, 1999, 2000, 2001 Free Software Foundation,
Inc.
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
Foundation, Inc.
This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.
......@@ -71,8 +71,9 @@ Compilers and Options
the `configure' script does not know about. Run `./configure --help'
for details on some of the pertinent environment variables.
You can give `configure' initial values for variables by setting
them in the environment. You can do that on the command line like this:
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
is an example:
./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
......@@ -137,9 +138,10 @@ Specifying the System Type
==========================
There may be some features `configure' cannot figure out
automatically, but needs to determine by the type of host the package
will run on. Usually `configure' can figure that out, but if it prints
a message saying it cannot guess the host type, give it the
automatically, but needs to determine by the type of machine the package
will run on. Usually, assuming the package is built to be run on the
_same_ architectures, `configure' can figure that out, but if it prints
a message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
......@@ -151,20 +153,16 @@ where SYSTEM can have one of these forms:
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
need to know the host type.
need to know the machine type.
If you are _building_ compiler tools for cross-compiling, you should
use the `--target=TYPE' option to select the type of system they will
produce code for.
If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the host
platform (i.e., that on which the generated programs will eventually be
run) with `--host=TYPE'. In this case, you should also specify the
build platform with `--build=TYPE', because, in this case, it may not
be possible to guess the build platform (it sometimes involves
compiling and running simple test programs, and this can't be done if
the compiler is a cross compiler).
platform different from the build platform, you should specify the
"host" platform (i.e., that on which the generated programs will
eventually be run) with `--host=TYPE'.
Sharing Defaults
================
......
Makefile.am 100644 → 100755
View file @ 7d894615
......@@ -2,9 +2,9 @@
# Makefile.am
#
#
# Part of TREE-PUZZLE 5.2 (July 2004)
# Part of TREE-PUZZLE 5.2 (February 2005)
#
# (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
# (c) 2003-2005 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
......
Makefile.in deleted 100644 → 0
View file @ a74762f0
# Makefile.in generated by automake 1.6.1 from Makefile.am.
# @configure_input@
# Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002
# Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# This program is distributed in the hope that it will be useful,
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# (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
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......@@ -21,7 +21,7 @@ The corresponding parameters can be inferred from the data set.
INSTALLATION
For compile an intall instructions see INSTALL and doc/manual.html
For compile and install 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
......
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dnl $Id$
dnl
dnl configure.ac
dnl
dnl
dnl Part of TREE-PUZZLE 5.2 (February 2005)
dnl
dnl (c) 2003-2005 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
dnl (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer,
dnl M. Vingron, and Arndt von Haeseler
dnl (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
dnl
dnl All parts of the source except where indicated are distributed under
dnl the GNU public licence. See http://www.opensource.org for details.
dnl
dnl ($Id$)
dnl
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_INIT([tree-puzzle], [5.3.rc16])
AC_CANONICAL_BUILD
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE(tree-puzzle, 5.2)
AM_CONFIG_HEADER(src/config.h)
AM_INIT_AUTOMAKE
dnl AM_INIT_AUTOMAKE(tree-puzzle, 5.3.rc11)
AC_CONFIG_HEADERS(src/config.h)
dnl Gets build and target system type.
......@@ -24,7 +40,7 @@ dnl ---------------------------------------------------------------------
dnl Test function to test whether mpicc works correctly
dnl ---------------------------------------------------------------------
AC_DEFUN(AC_TEST_MPICC,[dnl
AC_DEFUN([AC_TEST_MPICC],[dnl
if test "$1" != "" ; then
if test "$MPICCSET" = "" ; then
cat > conftest.c <<EOF
......@@ -98,7 +114,7 @@ dnl ---------------------------------------------------------------------
dnl Test function to test whether the compiler handles quotes correctly
dnl ---------------------------------------------------------------------
AC_DEFUN(AC_TEST_CCQUOTES,[dnl
AC_DEFUN([AC_TEST_CCQUOTES],[dnl
if test "$1" != "" ; then
cat > conftest.c <<EOF
#include<stdio.h>
......@@ -164,4 +180,5 @@ 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])
dnl AC_CONFIG_FILES([Makefile src/Makefile src/sprng/Makefile doc/Makefile doc/fig/Makefile data/Makefile tests/Makefile])
AC_OUTPUT
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......@@ -2,9 +2,9 @@
# Makefile.am
#
#
# Part of TREE-PUZZLE 5.2 (July 2004)
# Part of TREE-PUZZLE 5.2 (February 2005)
#
# (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
# (c) 2003-2005 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
......
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# Makefile.in generated by automake 1.6.1 from Makefile.am.
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# This program is distributed in the hope that it will be useful,
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# (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
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data/atp6.a 100644 → 100755
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data/globin.a 100644 → 100755
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