Commit f12a8dc0 authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 1.2.3

parent bacfc626
2012-04-25 Release 1.1.0
2016-07-20 Release 1.2.3 (AndreaGiacomo, r313)
- fixed consensus line in ClustalW format, 'H' in NHQK not recognised as strong (bug in Squid)
(no new command-line flags)
2016-07-01 Release 1.2.2 (AndreaGiacomo, r310)
- fixed a memory leak in hhalign
- parallelised hhalign
- increased MAC-RAM default from 2GB to 8GB
(no new command-line flags)
2014-02-28 Release 1.2.1 (AndreaGiacomo, r292)
- corrected Clustal format consensus line
- label justification (multi-bit)
2013-06-12 Release 1.2.0 (AndreaGiacomo, r284)
--is-profile disable check if profile, force profile (default no)
--use-kimura use Kimura distance correction for aligned sequences (default no)
--percent-id convert distances into percent identities (default no)
fixed bug in --output-order=tree-order for pair-wise alignment
Kimura distance correction no longer default for protein
fixed bug in Viterbi algorithm (predominantly affected long nucleotide but also protein, to lesser extent)
Viterbi is less (~10x) memory hungry than MAC but still scales quadratically with length:
2GB of RAM (ClustalO default) can align sequences of 6.5k residues with MAC and 18k with Viterbi
8GB of RAM (EBI limit) can align sequences of 12.5k residues with MAC and 37k with Viterbi
A Viterbi alignment of sequences of 100k residues will require 59GB of RAM
2013-05-16 Release 1.1.1 (r281)
--cluster-size=<n> soft maximum of sequences in sub-clusters
--clustering-out=<file> Clustering output file
--residuenumber, --resno in Clustal format print residue numbers (default no)
--wrap=<n> number of residues before line-wrap in output
--output-order={input-order,tree-order} MSA output order like in input/guide-tree
turned off Kimura correction for DNA/RNA
enable distance matrix output after initial mBed but subsequent full distance calculation
enable termination after distance/guide-tree calculation (--max-hmm-iterations=-1)
longer sequence labels
2012-04-25 Release 1.1.0 (FilumVitae, r275)
DNA and RNA support now added. Sequence type can be specified manually
using --seqtype={Protein|DNA|RNA}
2012-03-27 Release 1.0.4
2012-03-27 Release 1.0.4 (r273)
zipped input now supported
2011-09-07 Release 1.0.3
2011-09-07 Release 1.0.3 (r263)
Bugs fixed:
......@@ -27,11 +83,21 @@ Bugs fixed:
doxygen documentation fixes and fix of API example
introduced MAC-RAM flag to set amount of RAM given to MAC (in MB)
2011-06-23 Release 1.0.2
2011-06-17 Release 1.0.0 (DeshilHollesEamus)
2011-06-17 Release 1.0.0 (DeshilHollesEamus, r250)
2011-04-14 Release 0.2.0 (IbiMeVidebunt, r238)
2010-06-17 Release 0.0.1 (Dubliniensis)
2011-03-23 Release 0.1.1 (OppidumLeonis, r224)
2011-02-22 Release 0.1.0 (OppidumLeonis, r200)
2010-08-10 Release 0.0.3 (Thamesis, r120)
2010-06-17 Release 0.0.1 (Dubliniensis, r81)
First "release" as program has been able for a while to perform
all basic tasks without problems.
......
......@@ -31,7 +31,7 @@ PROJECT_NAME = "Clustal Omega"
# This could be handy for archiving the generated documentation or
# if some version control system is used.
PROJECT_NUMBER = 1.2.2
PROJECT_NUMBER = 1.2.3
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
# base path where the generated documentation will be put.
......
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.63 for Clustal Omega 1.2.2.
# Generated by GNU Autoconf 2.63 for Clustal Omega 1.2.3.
#
# Report bugs to <clustalw@ucd.ie>.
#
......@@ -745,8 +745,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='Clustal Omega'
PACKAGE_TARNAME='clustal-omega'
PACKAGE_VERSION='1.2.2'
PACKAGE_STRING='Clustal Omega 1.2.2'
PACKAGE_VERSION='1.2.3'
PACKAGE_STRING='Clustal Omega 1.2.3'
PACKAGE_BUGREPORT='clustalw@ucd.ie'
# Factoring default headers for most tests.
......@@ -1483,7 +1483,7 @@ if test "$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 Clustal Omega 1.2.2 to adapt to many kinds of systems.
\`configure' configures Clustal Omega 1.2.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
......@@ -1553,7 +1553,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of Clustal Omega 1.2.2:";;
short | recursive ) echo "Configuration of Clustal Omega 1.2.3:";;
esac
cat <<\_ACEOF
......@@ -1659,7 +1659,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
Clustal Omega configure 1.2.2
Clustal Omega configure 1.2.3
generated by GNU Autoconf 2.63
Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
......@@ -1673,7 +1673,7 @@ 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 Clustal Omega $as_me 1.2.2, which was
It was created by Clustal Omega $as_me 1.2.3, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ $0 $@
......@@ -2492,7 +2492,7 @@ fi
# Define the identity of the package.
PACKAGE='clustal-omega'
VERSION='1.2.2'
VERSION='1.2.3'
cat >>confdefs.h <<_ACEOF
......@@ -21790,7 +21790,7 @@ exec 6>&1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by Clustal Omega $as_me 1.2.2, which was
This file was extended by Clustal Omega $as_me 1.2.3, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
......@@ -21853,7 +21853,7 @@ Report bugs to <bug-autoconf@gnu.org>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_version="\\
Clustal Omega config.status 1.2.2
Clustal Omega config.status 1.2.3
configured by $0, generated by GNU Autoconf 2.63,
with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
......
# configure.ac for Clustal Omega
#
# RCS $Id: configure.ac 310 2016-06-13 14:11:35Z fabian $
# RCS $Id: configure.ac 313 2016-07-20 13:30:29Z fabian $
# release
......@@ -28,7 +28,11 @@
#PACKAGE_CODENAME="AndreaGiacomo"
#AC_INIT([Clustal Omega], [1.2.1], [clustalw@ucd.ie])
#PACKAGE_CODENAME="AndreaGiacomo"
AC_INIT([Clustal Omega], [1.2.2], [clustalw@ucd.ie])
# r310
#AC_INIT([Clustal Omega], [1.2.2], [clustalw@ucd.ie])
#PACKAGE_CODENAME="AndreaGiacomo"
# r313
AC_INIT([Clustal Omega], [1.2.3], [clustalw@ucd.ie])
PACKAGE_CODENAME="AndreaGiacomo"
# The AC_INIT macro can take any source file as an argument. It just
......
......@@ -228,7 +228,7 @@
/* Define to the full name and version of this package. */
#ifndef CLUSTAL_OMEGA_PACKAGE_STRING
#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.2.2"
#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.2.3"
#endif
/* Define to the one symbol short name of this package. */
......@@ -238,7 +238,7 @@
/* Define to the version of this package. */
#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION
#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.2.2"
#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.2.3"
#endif
/* The size of `fpos_t', as computed by sizeof. */
......@@ -301,7 +301,7 @@
/* Version number of package */
#ifndef CLUSTAL_OMEGA_VERSION
#define CLUSTAL_OMEGA_VERSION "1.2.2"
#define CLUSTAL_OMEGA_VERSION "1.2.3"
#endif
/* Define if using the dmalloc debugging malloc package */
......
......@@ -14,7 +14,7 @@
* formatted files. Derivative of msf.c; MSF is a pretty
* generic interleaved format.
*
* RCS $Id: clustal.c 291 2014-02-27 18:20:54Z fabian $ (Original squid RCS Id: clustal.c,v 1.1 1999/07/15 22:26:53 eddy Exp)
* RCS $Id: clustal.c 312 2016-07-14 16:57:39Z fabian $ (Original squid RCS Id: clustal.c,v 1.1 1999/07/15 22:26:53 eddy Exp)
*/
#include <stdbool.h>
......@@ -343,7 +343,7 @@ WriteClustal(FILE *fp, MSA *msa)
case 'K': strong_bins[1]++; strong_bins[2]++; strong_bins[4]++; break;
case 'D': strong_bins[3]++; break;
case 'R': strong_bins[4]++; break;
case 'H': strong_bins[4]++; strong_bins[7]++; break;
case 'H': strong_bins[2]++; strong_bins[4]++; strong_bins[7]++; break; /* added bin-2 (NHQK), FS 2016-07-14 */
case 'M': strong_bins[5]++; strong_bins[6]++; break;
case 'I': strong_bins[5]++; strong_bins[6]++; break;
case 'L': strong_bins[5]++; strong_bins[6]++; break;
......@@ -377,7 +377,7 @@ WriteClustal(FILE *fp, MSA *msa)
case 'A': weak_bins[0]++; weak_bins[1]++; weak_bins[2]++; weak_bins[4]++; break;
case 'T': weak_bins[1]++; weak_bins[3]++; weak_bins[4]++; break;
case 'V': weak_bins[1]++; weak_bins[9]++; break;
case 'G': weak_bins[2]++; break;
case 'G': weak_bins[2]++; weak_bins[5]++; break; /* Added bin-5, FS 2016-07-14 */
case 'N': weak_bins[3]++; weak_bins[5]++; weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
case 'K': weak_bins[3]++; weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
case 'D': weak_bins[5]++; weak_bins[6]++; weak_bins[7]++; break;
......
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