[med-svn] r4204 - in trunk/packages/clustalw/trunk: . debian
Charles Plessy
plessy at alioth.debian.org
Wed Oct 14 05:35:28 UTC 2009
Author: plessy
Date: 2009-10-14 05:35:26 +0000 (Wed, 14 Oct 2009)
New Revision: 4204
Added:
trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream
trunk/packages/clustalw/trunk/debian/tests.clustalw/
trunk/packages/clustalw/trunk/debian/upstream-metadata.yaml
Removed:
trunk/packages/clustalw/trunk/CHANGELOG
trunk/packages/clustalw/trunk/tests.clustalw/
Modified:
trunk/packages/clustalw/trunk/debian/changelog
trunk/packages/clustalw/trunk/debian/clustalw.1
trunk/packages/clustalw/trunk/debian/clustalw.1.xml
trunk/packages/clustalw/trunk/debian/clustalw.examples
trunk/packages/clustalw/trunk/debian/control
trunk/packages/clustalw/trunk/debian/copyright
trunk/packages/clustalw/trunk/debian/rules
Log:
Updated manpage, reorganised package, added metadata, refreshed copyright.
* Updated debian/watch to latest upstream names (Closes: #550895).
* debian/control:
- Incremented Standards-Version to reflect conformance with
Policy 3.8.3 (no changes needed).
- Removed the citation information from the package long description.
* Manpages debian/clustalw.1* refreshed.
* Updated debian/copyright to the latest experimentation on the format.
* Added various Upstream informations in debian/upstream-metadata.yaml.
* Moved the upstream changelog and the test data to the debian directory.
(debian/rules, debian/clustalw.examples).
Deleted: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/CHANGELOG 2009-10-14 05:35:26 UTC (rev 4204)
@@ -1,249 +0,0 @@
-----------------------------------------------------------------------
-Version 2.0.12
-----------------------------------------------------------------------
-
-* Fixed bug 189 "Fixed filename used for iteration":
-Now Creating temporary file and added error check
-
-* Fixed bug 180 "Pairwise NJ tree: final bracket missing"
-
-* Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity":
- Using relative error now to avoid unsafe comparison which led to
- incorrect branching
-
-* Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"
-
-* Fixed bug 162 "percent identity file option in clustalW not working":
-Added -pim as command line option. See help
-
-* Fixed bug 155 "upgma trees cannot be read"
-
-* Fixed bug 147 "report duplicate sequences":
- "ClustalW/X now report offending sequences which are empty, duplicates etc
-
-* Fixed bug 134 "Exit when encountering unrecognized cmdline params":
-ClustalW now exits when encountering invalid values for command line
-arguments instead of just reverting to default values
-
-* Fixed bug 185 "clustal alignments differ between interactive and commandline mode"
-window-gap and ktuple initialisation now fixed and made the same
-between commandline and interactive mode
-
-* Fixed bug 184 "error messages are send to stdout"
-
-* Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA
- code (see RootedGuideTree.cpp)
-
-* General code cleanup
-- Introduced return values where control reached end of non-void function
-- Removed unused variables
-- Removed comparison between signed and unsigned integer expressions
-- Removed deprecated conversion from string constant to char*
-
-
-
-----------------------------------------------------------------------
-Version 2.0.11
-----------------------------------------------------------------------
-
-* fixed file extension bug 166 in interactive mode
-
-* Fixed bug 169, memory violation for DNA/RNA k-tuple
-
-* Cut down distance calculation, symmetric matrix
-
-
-----------------------------------------------------------------------
-Version 2.0.10
-----------------------------------------------------------------------
-
-* Fixed g++-4.3 compilation errors
-
-* Added new -quiet command line flag
-
-* Added new -stats=<file> command line flag
-
-* Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms
-
-* Fixed bug 141: profile merging and saving failed
-
-* Fixed bug 139: saving of column quality scores
-
-* Updated help files (new flags, new colour parameter format)
-
-
-----------------------------------------------------------------------
-Version 2.0.9
-----------------------------------------------------------------------
-
-* GUI now responding and giving feedback during alignment
-
-* automatic automake os detection
-
-* new OS_ define (set by clustalw/configure clustalx/clustalx.pro)
-
-* got rid of qt3 dependencies
-
-* removed QScrollArea bug workaround (fixed in Qt 4.3)
-
-* Fixed bug 135: Last sequence and last residue not displayed on MacOSX
-
-* Fixed bug 123: secondary structure profile alignment in clustalX on Mac
-
-* Fixed g++-4.3 build error (include climits.h)
-
-
-----------------------------------------------------------------------
-Version 2.0.8
-----------------------------------------------------------------------
-
-* Implemented maxseqlen cmdline switch
-
-* Updated help-file
-
-* Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)
-
-* Fixed bug 133: providing profiles on command line fails (ClustalX)
-
-* Fixed bug 125: Angle bracket inside sequence
-
-* Fixed bug 129: Early exit on empty sequence
-
-* Fixed a couple of possible memory leaks
-
-
-----------------------------------------------------------------------
-Version 2.0.7
-----------------------------------------------------------------------
-
-* Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed
-
-* Fixed bug 122: convert option broken
-
-* Fixed reopened bug 114: profile alignment input didn't work with new
- getSeqRange routines
-
-* Fixed bug 119: build with g++ 4.3
-
-----------------------------------------------------------------------
-Version 2.0.6
-----------------------------------------------------------------------
-
-* Fixed bug 77: fasta input performance issue
-
-* Fixed bug 114: segfault while doing profile alignment with secondary
- structure mask
-
-* Removed unncessary id console output in EMBLFileParser.cpp
-
-* Fixed Bugs 108 and 109 and allowed mixed-case command line options
-
-
-----------------------------------------------------------------------
-Version 2.0.5
-----------------------------------------------------------------------
-
-* Fixed bug 105: Disallowed combination of "Reset Gaps"
- and Iteration in GUI
-
-* Fixed bug 104 "reset all gaps doesn't work"
-
-* Changed command line separator for Mac to hyphen instead slash
-
-* Fixed full command line parsing for ClustalX after help flag
-
-
-----------------------------------------------------------------------
-Version 2.0.4
-----------------------------------------------------------------------
-
-* Updated URLs in help files
-
-* Fixed bug 96: error message when loading alignment with identical
- sequence names
-
-* Made console output look more like 1.83
-
-* Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83"
- getMatrix was called with wrong scaling factor
-
-* Fixed bug 99: "stars in input not ignored"
- Asterisks were changed to gaps in alignment
-
-* New command line option: -fullhelp which dumps the built-in help
- file content.
-
-* Quickfix for bug 94 "quicktree seqfault"
-
-
-----------------------------------------------------------------------
-<= Version 2.0.3
-----------------------------------------------------------------------
-
-* Added LICENSE file to distribution
-This file contains the information about commercial licensing of
-clustal as well as FAQ for licensing issues
-
-* Added README file to distribution
-This is the file that lists the files and directories on the Clustal
-FTP site. It also includes acknowledgements of people who have
-contributed binaries
-
-* Removed .pro Qt file from the distribution
-pro-file should be generated anew using qmake and modified according
-to build requirements, i.e. no need for version control.
-
-* Fixed bug where ClustalX2 was not processing command line args
-
-* Fixed Segfault on opening helpfile. Happened on Linux only with -O2
-and when calling binary directly, not using the wrapper
-
-* Added debian packaging files
-
-* Added support for help command line flag GUI/xmenus version
-When requesting help file, graphical version of command line help is
-displayed (1.83 tried to open clustalw help)
-
-* Added complete automake (configure etc) system according to the
-following websites:
-- http://www.openismus.com/documents/linux/automake/automake.shtml
-- http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
-
-* clustalw files source files have been moved to subdir
-
-* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30.
-This fixes problem of large amount of space between sequence name and
-actual alignment in clustal output files
-
-* This solves bug #72 with long lines (5000+) in fasta files
-changed code to use strings rather than arrays. Needed to add delim
-parameter to getline in order to read files formatted for different
-OSs on different platforms.
-
-* Fixed Bug 79:
-"The count of amino acids in the ClustalX Postscript output not correct"
-Off-by-one issue
-
-* ClustalX and ClustalW version numbers are now the same and defined in
-ClustalW code (automake)
-
-* Fixed problem with compilation of ClustalX2 with gcc3
-avoiding gcc3 error message: cannot declare member function
-QDir::currentPath'
-
-* Target now clustalw2 instead of clustalw
-
-* Fixed Bug 46
-added in aminoacid code O for pyrrolysine
-
-* Fixed bug 89
-changed clustalw2.0 to conform to 1.83 behaviour for width of sequence
-ID and alignment
-
-* Fixed bug 90
-changed clustalw2.0 to conform to 1.83 behaviour leading spaces are
-stripped from FASTA identifiers.
-
-* Fixed bug 91
-Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
-numbers and spaces.
Copied: trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream (from rev 4203, trunk/packages/clustalw/trunk/CHANGELOG)
===================================================================
--- trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream (rev 0)
+++ trunk/packages/clustalw/trunk/debian/CHANGELOG.upstream 2009-10-14 05:35:26 UTC (rev 4204)
@@ -0,0 +1,249 @@
+----------------------------------------------------------------------
+Version 2.0.12
+----------------------------------------------------------------------
+
+* Fixed bug 189 "Fixed filename used for iteration":
+Now Creating temporary file and added error check
+
+* Fixed bug 180 "Pairwise NJ tree: final bracket missing"
+
+* Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity":
+ Using relative error now to avoid unsafe comparison which led to
+ incorrect branching
+
+* Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"
+
+* Fixed bug 162 "percent identity file option in clustalW not working":
+Added -pim as command line option. See help
+
+* Fixed bug 155 "upgma trees cannot be read"
+
+* Fixed bug 147 "report duplicate sequences":
+ "ClustalW/X now report offending sequences which are empty, duplicates etc
+
+* Fixed bug 134 "Exit when encountering unrecognized cmdline params":
+ClustalW now exits when encountering invalid values for command line
+arguments instead of just reverting to default values
+
+* Fixed bug 185 "clustal alignments differ between interactive and commandline mode"
+window-gap and ktuple initialisation now fixed and made the same
+between commandline and interactive mode
+
+* Fixed bug 184 "error messages are send to stdout"
+
+* Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA
+ code (see RootedGuideTree.cpp)
+
+* General code cleanup
+- Introduced return values where control reached end of non-void function
+- Removed unused variables
+- Removed comparison between signed and unsigned integer expressions
+- Removed deprecated conversion from string constant to char*
+
+
+
+----------------------------------------------------------------------
+Version 2.0.11
+----------------------------------------------------------------------
+
+* fixed file extension bug 166 in interactive mode
+
+* Fixed bug 169, memory violation for DNA/RNA k-tuple
+
+* Cut down distance calculation, symmetric matrix
+
+
+----------------------------------------------------------------------
+Version 2.0.10
+----------------------------------------------------------------------
+
+* Fixed g++-4.3 compilation errors
+
+* Added new -quiet command line flag
+
+* Added new -stats=<file> command line flag
+
+* Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms
+
+* Fixed bug 141: profile merging and saving failed
+
+* Fixed bug 139: saving of column quality scores
+
+* Updated help files (new flags, new colour parameter format)
+
+
+----------------------------------------------------------------------
+Version 2.0.9
+----------------------------------------------------------------------
+
+* GUI now responding and giving feedback during alignment
+
+* automatic automake os detection
+
+* new OS_ define (set by clustalw/configure clustalx/clustalx.pro)
+
+* got rid of qt3 dependencies
+
+* removed QScrollArea bug workaround (fixed in Qt 4.3)
+
+* Fixed bug 135: Last sequence and last residue not displayed on MacOSX
+
+* Fixed bug 123: secondary structure profile alignment in clustalX on Mac
+
+* Fixed g++-4.3 build error (include climits.h)
+
+
+----------------------------------------------------------------------
+Version 2.0.8
+----------------------------------------------------------------------
+
+* Implemented maxseqlen cmdline switch
+
+* Updated help-file
+
+* Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)
+
+* Fixed bug 133: providing profiles on command line fails (ClustalX)
+
+* Fixed bug 125: Angle bracket inside sequence
+
+* Fixed bug 129: Early exit on empty sequence
+
+* Fixed a couple of possible memory leaks
+
+
+----------------------------------------------------------------------
+Version 2.0.7
+----------------------------------------------------------------------
+
+* Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed
+
+* Fixed bug 122: convert option broken
+
+* Fixed reopened bug 114: profile alignment input didn't work with new
+ getSeqRange routines
+
+* Fixed bug 119: build with g++ 4.3
+
+----------------------------------------------------------------------
+Version 2.0.6
+----------------------------------------------------------------------
+
+* Fixed bug 77: fasta input performance issue
+
+* Fixed bug 114: segfault while doing profile alignment with secondary
+ structure mask
+
+* Removed unncessary id console output in EMBLFileParser.cpp
+
+* Fixed Bugs 108 and 109 and allowed mixed-case command line options
+
+
+----------------------------------------------------------------------
+Version 2.0.5
+----------------------------------------------------------------------
+
+* Fixed bug 105: Disallowed combination of "Reset Gaps"
+ and Iteration in GUI
+
+* Fixed bug 104 "reset all gaps doesn't work"
+
+* Changed command line separator for Mac to hyphen instead slash
+
+* Fixed full command line parsing for ClustalX after help flag
+
+
+----------------------------------------------------------------------
+Version 2.0.4
+----------------------------------------------------------------------
+
+* Updated URLs in help files
+
+* Fixed bug 96: error message when loading alignment with identical
+ sequence names
+
+* Made console output look more like 1.83
+
+* Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83"
+ getMatrix was called with wrong scaling factor
+
+* Fixed bug 99: "stars in input not ignored"
+ Asterisks were changed to gaps in alignment
+
+* New command line option: -fullhelp which dumps the built-in help
+ file content.
+
+* Quickfix for bug 94 "quicktree seqfault"
+
+
+----------------------------------------------------------------------
+<= Version 2.0.3
+----------------------------------------------------------------------
+
+* Added LICENSE file to distribution
+This file contains the information about commercial licensing of
+clustal as well as FAQ for licensing issues
+
+* Added README file to distribution
+This is the file that lists the files and directories on the Clustal
+FTP site. It also includes acknowledgements of people who have
+contributed binaries
+
+* Removed .pro Qt file from the distribution
+pro-file should be generated anew using qmake and modified according
+to build requirements, i.e. no need for version control.
+
+* Fixed bug where ClustalX2 was not processing command line args
+
+* Fixed Segfault on opening helpfile. Happened on Linux only with -O2
+and when calling binary directly, not using the wrapper
+
+* Added debian packaging files
+
+* Added support for help command line flag GUI/xmenus version
+When requesting help file, graphical version of command line help is
+displayed (1.83 tried to open clustalw help)
+
+* Added complete automake (configure etc) system according to the
+following websites:
+- http://www.openismus.com/documents/linux/automake/automake.shtml
+- http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+* clustalw files source files have been moved to subdir
+
+* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30.
+This fixes problem of large amount of space between sequence name and
+actual alignment in clustal output files
+
+* This solves bug #72 with long lines (5000+) in fasta files
+changed code to use strings rather than arrays. Needed to add delim
+parameter to getline in order to read files formatted for different
+OSs on different platforms.
+
+* Fixed Bug 79:
+"The count of amino acids in the ClustalX Postscript output not correct"
+Off-by-one issue
+
+* ClustalX and ClustalW version numbers are now the same and defined in
+ClustalW code (automake)
+
+* Fixed problem with compilation of ClustalX2 with gcc3
+avoiding gcc3 error message: cannot declare member function
+QDir::currentPath'
+
+* Target now clustalw2 instead of clustalw
+
+* Fixed Bug 46
+added in aminoacid code O for pyrrolysine
+
+* Fixed bug 89
+changed clustalw2.0 to conform to 1.83 behaviour for width of sequence
+ID and alignment
+
+* Fixed bug 90
+changed clustalw2.0 to conform to 1.83 behaviour leading spaces are
+stripped from FASTA identifiers.
+
+* Fixed bug 91
+Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
+numbers and spaces.
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/changelog 2009-10-14 05:35:26 UTC (rev 4204)
@@ -1,12 +1,20 @@
-clustalw (2.0.12-1) UNRELEASED; urgency=low
+clustalw (2.0.12-1) unstable; urgency=low
* New upstream release fixing many bugs
- (see /usr/share/doc/clustalw CHANGELOG).
- * Updated debian/watch to latest upstream names.
+ (see /usr/share/doc/clustalw/CHANGELOG).
+ * Updated debian/watch to latest upstream names (Closes: #550895).
* debian/control:
- Added ${misc:Depends} substitition variable.
+ - Incremented Standards-Version to reflect conformance with
+ Policy 3.8.3 (no changes needed).
+ - Removed the citation information from the package long description.
+ * Manpages debian/clustalw.1* refreshed.
+ * Updated debian/copyright to the latest experimentation on the format.
+ * Added various Upstream informations in debian/upstream-metadata.yaml.
+ * Moved the upstream changelog and the test data to the debian directory.
+ (debian/rules, debian/clustalw.examples).
- -- Charles Plessy <plessy at debian.org> Mon, 28 Sep 2009 15:56:36 +0900
+ -- Charles Plessy <plessy at debian.org> Wed, 14 Oct 2009 13:47:28 +0900
clustalw (2.0.10-1) unstable; urgency=low
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1 2009-10-14 05:35:26 UTC (rev 4204)
@@ -1,21 +1,29 @@
+'\" t
.\" Title: CLUSTALW
.\" Author: Des Higgins
-.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 12/07/2008
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 10/14/2009
.\" Manual: Clustal Manual
-.\" Source: Clustal 2.0.10
+.\" Source: Clustal 2.0.12
+.\" Language: English
.\"
-.TH "CLUSTALW" "1" "12/07/2008" "Clustal 2.0.10" "Clustal Manual"
+.TH "CLUSTALW" "1" "10/14/2009" "Clustal 2.0.12" "Clustal Manual"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
.SH "NAME"
clustalw \- Multiple alignment of nucleic acid and protein sequences
.SH "SYNOPSIS"
-.HP 9
+.HP \w'\fBclustalw\fR\ 'u
\fBclustalw\fR [\fB\-infile\fR] \fIfile\&.ext\fR [\fBOPTIONS\fR]
-.HP 9
+.HP \w'\fBclustalw\fR\ 'u
\fBclustalw\fR [\fB\-help\fR | \fB\-fullhelp\fR]
.SH "DESCRIPTION"
.PP
@@ -62,6 +70,11 @@
Calculate NJ tree\&.
.RE
.PP
+\fB\-pim\fR
+.RS 4
+Output percent identity matrix (while calculating the tree)\&.
+.RE
+.PP
\fB \-bootstrap\fR\fB\fI=n\fR\fR\fB \fR
.RS 4
Bootstrap a NJ tree (\fIn\fR= number of bootstraps; def\&. = 1000)\&.
@@ -77,8 +90,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-General settings:
-.RS
+.ps +1
+\fBGeneral settings:\fR
+.RS 4
.PP
\fB\-interactive\fR
.RS 4
@@ -178,8 +192,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Fast Pairwise Alignments:
-.RS
+.ps +1
+\fBFast Pairwise Alignments:\fR
+.RS 4
.PP
\fB\-ktuple=\fR\fB\fIn\fR\fR
.RS 4
@@ -213,8 +228,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Slow Pairwise Alignments:
-.RS
+.ps +1
+\fBSlow Pairwise Alignments:\fR
+.RS 4
.PP
\fB\-pwmatrix=\fR
.RS 4
@@ -248,8 +264,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Multiple Alignments:
-.RS
+.ps +1
+\fBMultiple Alignments:\fR
+.RS 4
.PP
\fB\-newtree=\fR
.RS 4
@@ -350,8 +367,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Profile Alignments:
-.RS
+.ps +1
+\fBProfile Alignments:\fR
+.RS 4
.PP
\fB\-profile\fR
.RS 4
@@ -383,8 +401,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Sequence to Profile Alignments:
-.RS
+.ps +1
+\fBSequence to Profile Alignments:\fR
+.RS 4
.PP
\fB\-sequences\fR
.RS 4
@@ -406,8 +425,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Structure Alignments:
-.RS
+.ps +1
+\fBStructure Alignments:\fR
+.RS 4
.PP
\fB\-nosecstr1\fR
.RS 4
@@ -469,8 +489,9 @@
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
-Trees:
-.RS
+.ps +1
+\fBTrees:\fR
+.RS 4
.PP
\fB\-outputtree=\fR\fB\fInj\fR\fR\fB OR \fR\fB\fIphylip\fR\fR\fB OR \fR\fB\fIdist\fR\fR\fB OR \fR\fB\fInexus\fR\fR
.RS 4
@@ -504,111 +525,203 @@
.SH "BUGS"
.PP
The Clustal bug tracking system can be found at
-\fI\%http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal\fR\&.
+\m[blue]\fB\%http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal\fR\m[]\&.
.SH "SEE ALSO"
.PP
\fBclustalx\fR(1)\&.
.SH "REFERENCES"
.sp
.RS 4
-\h'-04'\(bu\h'+03'Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG\&. (2007)\&.
-\fIClustal W and Clustal X version 2\&.0\&.\fR\&[1]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG\&. (2007)\&.
+\m[blue]\fBClustal W and Clustal X version 2\&.0\&.\fR\m[]\&\s-2\u[1]\d\s+2
Bioinformatics, 23, 2947\-2948\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD\&. (2003)\&.
-\fIMultiple sequence alignment with the Clustal series of programs\&.\fR\&[2]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD\&. (2003)\&.
+\m[blue]\fBMultiple sequence alignment with the Clustal series of programs\&.\fR\m[]\&\s-2\u[2]\d\s+2
Nucleic Acids Res\&., 31, 3497\-3500\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ\&. (1998)\&.
-\fIMultiple sequence alignment with Clustal X\fR\&[3]\&. Trends Biochem Sci\&., 23, 403\-405\&.
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ\&. (1998)\&.
+\m[blue]\fBMultiple sequence alignment with Clustal X\fR\m[]\&\s-2\u[3]\d\s+2\&. Trends Biochem Sci\&., 23, 403\-405\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG\&. (1997)\&.
-\fIThe CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools\&.\fR\&[4]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG\&. (1997)\&.
+\m[blue]\fBThe CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools\&.\fR\m[]\&\s-2\u[4]\d\s+2
Nucleic Acids Res\&., 25, 4876\-4882\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Higgins DG, Thompson JD, Gibson TJ\&. (1996)\&.
-\fIUsing CLUSTAL for multiple sequence alignments\&.\fR\&[5]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Higgins DG, Thompson JD, Gibson TJ\&. (1996)\&.
+\m[blue]\fBUsing CLUSTAL for multiple sequence alignments\&.\fR\m[]\&\s-2\u[5]\d\s+2
Methods Enzymol\&., 266, 383\-402\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Thompson JD, Higgins DG, Gibson TJ\&. (1994)\&.
-\fICLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position\-specific gap penalties and weight matrix choice\&.\fR\&[6]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Thompson JD, Higgins DG, Gibson TJ\&. (1994)\&.
+\m[blue]\fBCLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position\-specific gap penalties and weight matrix choice\&.\fR\m[]\&\s-2\u[6]\d\s+2
Nucleic Acids Res\&., 22, 4673\-4680\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Higgins DG\&. (1994)\&.
-\fICLUSTAL V: multiple alignment of DNA and protein sequences\&.\fR\&[7]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Higgins DG\&. (1994)\&.
+\m[blue]\fBCLUSTAL V: multiple alignment of DNA and protein sequences\&.\fR\m[]\&\s-2\u[7]\d\s+2
Methods Mol Biol\&., 25, 307\-318
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Higgins DG, Bleasby AJ, Fuchs R\&. (1992)\&.
-\fICLUSTAL V: improved software for multiple sequence alignment\&.\fR\&[8]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Higgins DG, Bleasby AJ, Fuchs R\&. (1992)\&.
+\m[blue]\fBCLUSTAL V: improved software for multiple sequence alignment\&.\fR\m[]\&\s-2\u[8]\d\s+2
Comput\&. Appl\&. Biosci\&., 8, 189\-191\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Higgins,D\&.G\&. and Sharp,P\&.M\&. (1989)\&.
-\fIFast and sensitive multiple sequence alignments on a microcomputer\&.\fR\&[9]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Higgins,D\&.G\&. and Sharp,P\&.M\&. (1989)\&.
+\m[blue]\fBFast and sensitive multiple sequence alignments on a microcomputer\&.\fR\m[]\&\s-2\u[9]\d\s+2
Comput\&. Appl\&. Biosci\&., 5, 151\-153\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Higgins,D\&.G\&. and Sharp,P\&.M\&. (1988)\&.
-\fICLUSTAL: a package for performing multiple sequence alignment on a microcomputer\&.\fR\&[10]
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Higgins,D\&.G\&. and Sharp,P\&.M\&. (1988)\&.
+\m[blue]\fBCLUSTAL: a package for performing multiple sequence alignment on a microcomputer\&.\fR\m[]\&\s-2\u[10]\d\s+2
Gene, 73, 237\-244\&.
.RE
.SH "AUTHORS"
.PP
\fBDes Higgins\fR
-.sp -1n
-.IP "" 4
+.RS 4
Copyright holder for Clustal\&.
+.RE
.PP
\fBJulie Thompson\fR
-.sp -1n
-.IP "" 4
+.RS 4
Copyright holder for Clustal\&.
+.RE
.PP
\fBToby Gibson\fR
-.sp -1n
-.IP "" 4
+.RS 4
Copyright holder for Clustal\&.
+.RE
.PP
\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
-.sp -1n
-.IP "" 4
+.RS 4
Prepared this manpage in DocBook XML for the Debian distribution\&.
+.RE
.SH "COPYRIGHT"
-Copyright \(co 1988\(en2008 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
.br
-Copyright \(co 2008 Charles Plessy (This manpage)
+Copyright \(co 1988\(en2009 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
.br
+Copyright \(co 2008\(en2009 Charles Plessy (This manpage)
+.br
.PP
The binaries and source code are made available and can be distributed subject to the following conditions:
.sp
.RS 4
-\h'-04'\(bu\h'+03'Users are free to redistribute Clustal\ \&W or Clustal\ \&X in it\'s unmodified form as long as it is not for commercial gain\&.
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Users are free to redistribute Clustal\ \&W or Clustal\ \&X in it\'s unmodified form as long as it is not for commercial gain\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at
-<gibson at embl\&.de>
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at
+gibson at embl\&.de
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at
-<clustalw at ucd\&.ie>
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at
+clustalw at ucd\&.ie
where they will be considered for inclusion in future releases\&.
.RE
.PP
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2009-10-14 05:35:26 UTC (rev 4204)
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
+<?xml version='1.0' encoding='UTF-8'?>
<?xml-stylesheet type="text/xsl"
href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
@@ -18,7 +18,7 @@
<!ENTITY dhsurname "Plessy">
<!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "2.0.10">
+ <!ENTITY dhrelease "2.0.12">
<!ENTITY dhtitle "Clustal Manual">
<!ENTITY dhucpackage "CLUSTALW">
<!ENTITY dhpackage "clustalw">
@@ -60,11 +60,11 @@
</authorgroup>
<copyright>
<!-- I am unsure of the years, please correct me if I am wrong ! Charles -->
- <year>1988–2008</year>
+ <year>1988–2009</year>
<holder>Des Higgins, Julie Thompson & Toby Giboson (&dhproduct;)</holder>
</copyright>
<copyright>
- <year>2008</year>
+ <year>2008–2009</year>
<holder>&dhusername; (This manpage)</holder>
</copyright>
<legalnotice>
@@ -219,6 +219,15 @@
<varlistentry>
<term>
+ <option>-pim</option>
+ </term>
+ <listitem>
+ <para>Output percent identity matrix (while calculating the tree).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
<option>
-bootstrap<replaceable class="parameter">=n</replaceable>
</option>
Modified: trunk/packages/clustalw/trunk/debian/clustalw.examples
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.examples 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/clustalw.examples 2009-10-14 05:35:26 UTC (rev 4204)
@@ -1 +1 @@
-tests.clustalw
+debian/tests.clustalw
Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/control 2009-10-14 05:35:26 UTC (rev 4204)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
Build-Depends: debhelper (>= 7), cdbs, autotools-dev
-Standards-Version: 3.8.0
+Standards-Version: 3.8.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalw/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalw/trunk/
XS-Autobuild: yes
@@ -27,6 +27,3 @@
alignment editor like SeaView or within its companion Clustal X. When building
a model from your alignment, this can be applied for improved database
searches. The Debian package hmmer creates such in form of an HMM.
- .
- For details and citation purposes see paper "Clustal W and Clustal X version
- 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948
Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/copyright 2009-10-14 05:35:26 UTC (rev 4204)
@@ -1,80 +1,67 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
-Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
-X-Packaged-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
-X-Packaged-Date: Fri, 28 Aug 1998 16:09:48 +0200
-Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.12.tar.gz
+Name : Clustal W
+Contact : clustalw at ucd.ie
+Source : http://www.clustal.org/download/current/clustalw-2.0.12.tar.gz
+Disclamer :
+ This package is not part of the Debian operating system. The clustalw source
+ and binary Debian packages are part of the “non-free” area in our archive. The
+ packages in this area are not part of the Debian system, although they have
+ been configured for use with Debian. We nevertheless support the use of the
+ clustalw source and binary Debian packages and provide infrastructure for
+ non-free packages (such as our bug tracking system and mailing lists). The
+ licence does not forbid Debian from using autobuilders to create binary
+ packages.
-X-Non-Free-Disclamer: This package is not part of the Debian operating system.
- The clustalw source and binary Debian packages are part of the "non-free" area
- in our archive. The packages in this area are not part of the Debian system,
- although they have been configured for use with Debian. We nevertheless
- support the use of the clustalw source and binary Debian packages and provide
- infrastructure for non-free packages (such as our bug tracking system and
- mailing lists).
-X-Non-Free-Autobuild: yes
- The licence does not forbid Debian from using autobuilders to create binary
- packages.
-
-Files: *
-Copyright: © Des Higgins, Julie Thompson and Toby Gibson
-Licence: Not for commercial use, No modification of the code.
- Licensing ClustalW and ClustalX
- .
- Date:29 November 2007
- .
- The copyright for ClustalW and ClustalX is held by Des Higgins, Julie Thompson
- and Toby Gibson
- .
- The binaries and source code are made available and can be distributed subject
- to the following conditions:
- .
- Users are free to redistribute ClustalW or ClustalX in it's unmodified form as
- long as it is not for commercial gain.
- .
- Anyone wishing to redistribute Clustal commercially should contact Toby Gibson
- at gibson at embl.de
- .
- .
- If users make changes/have ideas that they believe would be useful to the
- broader research community they can send their suggestions to the clustal
- development team at clustalw at ucd.ie where they will be considered for inclusion
- in future releases.
-
-X-Comment: Frequently asked questions about Clustal licensing?
- ---------------------------------------------------
- .
+Copyright : © Des Higgins, Julie Thompson and Toby Gibson
+Licence : Not for commercial use, No modification of the code.
+
+ Date:29 November 2007
+
+ The copyright for ClustalW and ClustalX is held by Des Higgins, Julie Thompson
+ and Toby Gibson
+
+ The binaries and source code are made available and can be distributed subject
+ to the following conditions:
+
+ Users are free to redistribute ClustalW or ClustalX in it's unmodified form as
+ long as it is not for commercial gain.
+
+ Anyone wishing to redistribute Clustal commercially should contact Toby Gibson
+ at gibson at embl.de
+
+
+ If users make changes/have ideas that they believe would be useful to the
+ broader research community they can send their suggestions to the clustal
+ development team at clustalw at ucd.ie where they will be considered for inclusion
+ in future releases.
+
+Comment:
+
+ Frequently asked questions about Clustal licensing?
+ ---------------------------------------------------
+
1. Do I have to pay to use ClustalW or ClustalX?
No - unless you wish to redistribute Clustal for profit. In this case see question 4.
- .
+
2. Can I redistribute the Clustal binaries and source code?
Yes. We have always wanted to see Clustal have as wide a userbase and
distribution network as possible and are happy to see other sites host copies
of the official Clustal code.
- .
+
3. Can I make changes to the source code?
- .
+
You can make changes for your own purposes but you should not redistribute the
changed code.
- .
+
4. I want to include ClustalW/ClustalX in a commercial application who should I contact?
Toby Gibson at gibson at embl.de (also cc des.higgins at ucd.ie)
- .
+
5. There is no Clustal distribution for platform X. I have changed the code in
order to compile Clustal on this platform. Can I redistribute it?
- .
+
Ideally you should send us a copy of your source code changes as well as a
binary. We will include it in our contributed binaries section on our FTP site
along with an acknowledgement of your contribution.
-X-Comment: Modifications in the Debian package.
- I have received the following message from Des Higgins. -- Charles Plessy
- .
- "We are happy to give the Debian team permission to modify
- ClustalW 2 and ClustalX 2 code and redistribute the binaries as long as
- those modifications do not alter the algorithmic core, i.e. only affect
- installation routines, bug fixes etc. Please include the original
- LICENSE file into your package."
-
Files: debian/*
Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
© 2001 Dr. Guenter Bechly <gbechly at debian.org>
@@ -83,13 +70,20 @@
© 2006 Kai Hendry <hendry at iki.fi>
© 2007 Nelson A. de Oliveira <naoliv at debian.org>
© 2003-2008 Steffen Möller <moeller at debian.org>
- © 2007-2008 Charles Plessy <plessy at debian.org>
+ © 2007-2009 Charles Plessy <plessy at debian.org>
© 2008 David Paleino <d.paleino at gmail.com>
Licence: Unclear
The licence of the earlier works was never stated. Some works have been
obsoleted by release of version 2.0 — the lesstif migration for instance —
but authors are left in the list of copyright holders by courtesy. The work
of Charles Plessy and Steffen Möller can be treated as if it were public domain.
+Comment: I have received the following message from Des Higgins. -- Charles Plessy
+
+ "We are happy to give the Debian team permission to modify
+ ClustalW 2 and ClustalX 2 code and redistribute the binaries as long as
+ those modifications do not alter the algorithmic core, i.e. only affect
+ installation routines, bug fixes etc. Please include the original
+ LICENSE file into your package."
Files: debian/clustalw.1.xml, debian/clustalw.1
Copyright: © 2008 Charles Plessy <plessy at debian.org>
Modified: trunk/packages/clustalw/trunk/debian/rules
===================================================================
--- trunk/packages/clustalw/trunk/debian/rules 2009-10-12 10:23:59 UTC (rev 4203)
+++ trunk/packages/clustalw/trunk/debian/rules 2009-10-14 05:35:26 UTC (rev 4204)
@@ -4,6 +4,8 @@
include /usr/share/cdbs/1/class/autotools.mk
include /usr/share/cdbs/1/rules/debhelper.mk
+DEB_INSTALL_CHANGELOGS_ALL = debian/CHANGELOG.upstream
+
install/clustalw::
# We have to ask upstream if it is importnat for them that the binary is named clustalw2
mv $(CURDIR)/debian/clustalw/usr/bin/clustalw2 $(CURDIR)/debian/clustalw/usr/bin/clustalw
Added: trunk/packages/clustalw/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/clustalw/trunk/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/clustalw/trunk/debian/upstream-metadata.yaml 2009-10-14 05:35:26 UTC (rev 4204)
@@ -0,0 +1,23 @@
+Bugs: http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal
+Commercial: http://www.clustal.org/download/LICENSE
+Contact: clustalw at ucd.ie
+DOI: 10.1093/bioinformatics/btm404
+Homepage: http://www.clustal.org/
+PubMed: 17846036
+Reference: |
+ @article{M.A.Larkin11012007,
+ author = {Larkin, M.A. and Blackshields, G. and Brown, N.P. and Chenna, R. and McGettigan, P.A. and McWilliam, H. and Valentin, F. and Wallace, I.M. and Wilm, A. and Lopez, R. and Thompson, J.D. and Gibson, T.J. and Higgins, D.G.},
+ title = {{Clustal W and Clustal X version 2.0}},
+ journal = {Bioinformatics},
+ volume = {23},
+ number = {21},
+ pages = {2947-2948},
+ doi = {10.1093/bioinformatics/btm404},
+ year = {2007},
+ },
+ URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2947},
+ eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2947.pdf}
+ }
+Webservice:
+ - http://www.ebi.ac.uk/Tools/clustalw2/
+ - http://www.ch.embnet.org/software/ClustalW.html
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