[med-svn] r1818 - trunk/packages/clustalw/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Thu May 1 01:32:53 UTC 2008
Author: plessy
Date: 2008-05-01 01:32:52 +0000 (Thu, 01 May 2008)
New Revision: 1818
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/copyright
Log:
Almost ready for upload, but does not build with g++ 4.3
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-04-30 12:15:50 UTC (rev 1817)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-05-01 01:32:52 UTC (rev 1818)
@@ -1,9 +1,21 @@
-clustalw (2.0.5-2) UNRELEASED; urgency=low
+clustalw (2.0.6-1) UNRELEASED; urgency=low
- * Updated my email address.
+ [Charles Plessy]
+ * New upstream release:
+ - Bugs fixed (fasta input performance, segfault with secondary structure
+ mask)
+ - Allows mixed-case command line options.
+ - Removed unncessary id console output in EMBLFileParser.cpp
+ * Updated my email address (debian/control, debian/copyright,
+ debian/clustaw.1*).
- -- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 17:02:34 +0900
+ [Morten Kjeldgaard]
+ * debian/clustalw.1*: restored the introduction from Stéphane
+ Bortzmeyer original manpage.
+ * debian/copyright: updated information about the manpage.
+ -- Charles Plessy <plessy at debian.org> Thu, 01 May 2008 09:29:48 +0900
+
clustalw (2.0.5-1) unstable; urgency=low
* New upstream release (fixes problems with gaps).
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1 2008-04-30 12:15:50 UTC (rev 1817)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1 2008-05-01 01:32:52 UTC (rev 1818)
@@ -1,37 +1,37 @@
.\" Title: CLUSTALW
.\" Author: Des Higgins
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 04/30/2008
+.\" Date: 05/01/2008
.\" Manual: Clustal Manual
-.\" Source: Clustal 2.0.5
+.\" Source: Clustal 2.0.6
.\"
-.TH "CLUSTALW" "1" "04/30/2008" "Clustal 2.0.5" "Clustal Manual"
+.TH "CLUSTALW" "1" "05/01/2008" "Clustal 2.0.6" "Clustal Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-clustalw - Multiple alignment of nucleic acid and protein sequences
+clustalw \- Multiple alignment of nucleic acid and protein sequences
.SH "SYNOPSIS"
.HP 9
-\fBclustalw\fR [\fB\-infile\fR] \fIfile\.ext\fR [\fBOPTIONS\fR]
+\fBclustalw\fR [\fB\-infile\fR] \fIfile\&.ext\fR [\fBOPTIONS\fR]
.HP 9
\fBclustalw\fR [\fB\-help\fR | \fB\-fullhelp\fR]
.SH "DESCRIPTION"
.PP
-Clustal\ W is a general purpose multiple alignment program for DNA or proteins\.
+Clustal\ \&W is a general purpose multiple alignment program for DNA or proteins\&.
.PP
-The program performs simultaneous alignment of many nucleotide or amino acid sequences\. It is typically run interactively, providing a menu and an online help\. If you prefer to use it in command\-line (batch) mode, you will have to give several options, the minimum being
-\fB\-infile\fR\.
+The program performs simultaneous alignment of many nucleotide or amino acid sequences\&. It is typically run interactively, providing a menu and an online help\&. If you prefer to use it in command\-line (batch) mode, you will have to give several options, the minimum being
+\fB\-infile\fR\&.
.SH "OPTIONS"
.SS "DATA (sequences)"
.PP
-\fB \-infile=\fR\fB\fIfile\.ext\fR\fR\fB \fR
+\fB \-infile=\fR\fB\fIfile\&.ext\fR\fR\fB \fR
.RS 4
-Input sequences\.
+Input sequences\&.
.RE
.PP
-\fB \-profile1=\fR\fB\fIfile\.ext\fR\fR\fB and \-profile2=\fR\fB\fIfile\.ext\fR\fR\fB \fR
+\fB \-profile1=\fR\fB\fIfile\&.ext\fR\fR\fB and \-profile2=\fR\fB\fIfile\&.ext\fR\fR\fB \fR
.RS 4
Profiles (old alignment)
.RE
@@ -39,37 +39,37 @@
.PP
\fB\-options\fR
.RS 4
-List the command line parameters\.
+List the command line parameters\&.
.RE
.PP
\fB\-help or \-check\fR
.RS 4
-Outline the command line params\.
+Outline the command line params\&.
.RE
.PP
\fB\-fullhelp\fR
.RS 4
-Dump the built\-in help file content\.
+Dump the built\-in help file content\&.
.RE
.PP
\fB\-align\fR
.RS 4
-Do full multiple alignment\.
+Do full multiple alignment\&.
.RE
.PP
\fB\-tree\fR
.RS 4
-Calculate NJ tree\.
+Calculate NJ 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)\.
+Bootstrap a NJ tree (\fIn\fR= number of bootstraps; def\&. = 1000)\&.
.RE
.PP
\fB\-convert\fR
.RS 4
-Output the input sequences in a different file format\.
+Output the input sequences in a different file format\&.
.RE
.SS "PARAMETERS (set things)"
.sp
@@ -82,12 +82,12 @@
.PP
\fB\-interactive\fR
.RS 4
-Read command line, then enter normal interactive menus\.
+Read command line, then enter normal interactive menus\&.
.RE
.PP
\fB\-quicktree\fR
.RS 4
-Use FAST algorithm for the alignment guide tree\.
+Use FAST algorithm for the alignment guide tree\&.
.RE
.PP
\fB\-type=\fR
@@ -95,17 +95,17 @@
\fIPROTEIN\fR
or
\fIDNA\fR
-sequences\.
+sequences\&.
.RE
.PP
\fB\-negative\fR
.RS 4
-Protein alignment with negative values in matrix\.
+Protein alignment with negative values in matrix\&.
.RE
.PP
\fB\-outfile=\fR
.RS 4
-Sequence alignment file name\.
+Sequence alignment file name\&.
.RE
.PP
\fB\-output=\fR
@@ -115,7 +115,7 @@
\fIPHYLIP\fR,
\fIPIR\fR
or
-\fINEXUS\fR\.
+\fINEXUS\fR\&.
.RE
.PP
\fB\-outputorder=\fR
@@ -130,7 +130,7 @@
\fILOWER\fR
or
\fIUPPER\fR
-(for GDE output only)\.
+(for GDE output only)\&.
.RE
.PP
\fB\-seqnos=\fR
@@ -138,7 +138,7 @@
\fIOFF\fR
or
\fION\fR
-(for Clustal output only)\.
+(for Clustal output only)\&.
.RE
.PP
\fB\-seqnos_range=\fR
@@ -146,7 +146,7 @@
\fIOFF\fR
or
\fION\fR
-(NEW: for all output formats)\.
+(NEW: for all output formats)\&.
.RE
.PP
\fB\-range=\fR\fB\fIm\fR\fR\fB,\fR\fB\fIn\fR\fR
@@ -154,7 +154,7 @@
Sequence range to write starting
\fIm\fR
to
-\fIm\fR+\fIn\fR\.
+\fIm\fR+\fIn\fR\&.
.RE
.RE
.sp
@@ -167,29 +167,29 @@
.PP
\fB\-ktuple=\fR\fB\fIn\fR\fR
.RS 4
-Word size\.
+Word size\&.
.RE
.PP
\fB\-topdiags=\fR\fB\fIn\fR\fR
.RS 4
-Number of best diags\.
+Number of best diags\&.
.RE
.PP
\fB\-window=\fR\fB\fIn\fR\fR
.RS 4
-Window around best diags\.
+Window around best diags\&.
.RE
.PP
\fB\-pairgap=\fR\fB\fIn\fR\fR
.RS 4
-Gap penalty\.
+Gap penalty\&.
.RE
.PP
\fB\-score\fR
.RS 4
\fIPERCENT\fR
or
-\fIABSOLUTE\fR\.
+\fIABSOLUTE\fR\&.
.RE
.RE
.sp
@@ -214,17 +214,17 @@
.RS 4
DNA weight matrix=\fIBLOSUM\fRIUB,
\fIBLOSUM\fRCLUSTALW or
-\fIBLOSUM\fRfilename\.
+\fIBLOSUM\fRfilename\&.
.RE
.PP
\fB\-pwgapopen=\fR\fB\fIf\fR\fR
.RS 4
-Gap opening penalty\.
+Gap opening penalty\&.
.RE
.PP
\fB\-pwgapext=\fR\fB\fIf\fR\fR
.RS 4
-Gap extension penalty\.
+Gap extension penalty\&.
.RE
.RE
.sp
@@ -237,12 +237,12 @@
.PP
\fB\-newtree=\fR
.RS 4
-File for new guide tree\.
+File for new guide tree\&.
.RE
.PP
\fB\-usetree=\fR
.RS 4
-File for old guide tree\.
+File for old guide tree\&.
.RE
.PP
\fB\-matrix=\fR
@@ -252,7 +252,7 @@
\fIGONNET\fR,
\fIID\fR
or
-\fIfilename\fR\.
+\fIfilename\fR\&.
.RE
.PP
\fB\-dnamatrix=\fR
@@ -260,47 +260,47 @@
DNA weight matrix=\fIIUB\fR,
\fICLUSTALW\fR
or
-\fIfilename\fR\.
+\fIfilename\fR\&.
.RE
.PP
\fB\-gapopen=\fR\fB\fIf\fR\fR
.RS 4
-Gap opening penalty\.
+Gap opening penalty\&.
.RE
.PP
\fB\-gapext=\fR\fB\fIf\fR\fR
.RS 4
-Gap extension penalty\.
+Gap extension penalty\&.
.RE
.PP
\fB\-engaps\fR
.RS 4
-No end gap separation pen\.
+No end gap separation pen\&.
.RE
.PP
\fB\-gapdist=\fR\fB\fIn\fR\fR
.RS 4
-Gap separation pen\. range\.
+Gap separation pen\&. range\&.
.RE
.PP
\fB\-nogap\fR
.RS 4
-Residue\-specific gaps off\.
+Residue\-specific gaps off\&.
.RE
.PP
\fB\-nohgap\fR
.RS 4
-Hydrophilic gaps off\.
+Hydrophilic gaps off\&.
.RE
.PP
\fB\-hgapresidues=\fR
.RS 4
-List hydrophilic res\.
+List hydrophilic res\&.
.RE
.PP
\fB\-maxdiv=\fR\fB\fIn\fR\fR
.RS 4
-Percent identity for delay\.
+Percent identity for delay\&.
.RE
.PP
\fB\-type=\fR
@@ -312,7 +312,7 @@
.PP
\fB\-transweight=\fR\fB\fIf\fR\fR
.RS 4
-Transitions weighting\.
+Transitions weighting\&.
.RE
.PP
\fB\-iteration=\fR
@@ -321,12 +321,12 @@
or
\fITREE\fR
or
-\fIALIGNMENT\fR\.
+\fIALIGNMENT\fR\&.
.RE
.PP
\fB\-numiter=\fR\fB\fIn\fR\fR
.RS 4
-Maximum number of iterations to perform\.
+Maximum number of iterations to perform\&.
.RE
.RE
.sp
@@ -339,27 +339,27 @@
.PP
\fB\-profile\fR
.RS 4
-Merge two alignments by profile alignment\.
+Merge two alignments by profile alignment\&.
.RE
.PP
\fB\-newtree1=\fR
.RS 4
-File for new guide tree for profile1\.
+File for new guide tree for profile1\&.
.RE
.PP
\fB\-newtree2=\fR
.RS 4
-File for new guide tree for profile2\.
+File for new guide tree for profile2\&.
.RE
.PP
\fB\-usetree1=\fR
.RS 4
-File for old guide tree for profile1\.
+File for old guide tree for profile1\&.
.RE
.PP
\fB\-usetree2=\fR
.RS 4
-File for old guide tree for profile2\.
+File for old guide tree for profile2\&.
.RE
.RE
.sp
@@ -372,17 +372,17 @@
.PP
\fB\-sequences\fR
.RS 4
-Sequentially add profile2 sequences to profile1 alignment\.
+Sequentially add profile2 sequences to profile1 alignment\&.
.RE
.PP
\fB\-newtree=\fR
.RS 4
-File for new guide tree\.
+File for new guide tree\&.
.RE
.PP
\fB\-usetree=\fR
.RS 4
-File for old guide tree\.
+File for old guide tree\&.
.RE
.RE
.sp
@@ -395,57 +395,57 @@
.PP
\fB\-nosecstr1\fR
.RS 4
-Do not use secondary structure\-gap penalty mask for profile 1\.
+Do not use secondary structure\-gap penalty mask for profile 1\&.
.RE
.PP
\fB\-nosecstr2\fR
.RS 4
-Do not use secondary structure\-gap penalty mask for profile 2\.
+Do not use secondary structure\-gap penalty mask for profile 2\&.
.RE
.PP
\fB\-secstrout=\fR\fB\fISTRUCTURE\fR\fR\fB or \fR\fB\fIMASK\fR\fR\fB or \fR\fB\fIBOTH\fR\fR\fB or \fR\fB\fINONE\fR\fR
.RS 4
-Output in alignment file\.
+Output in alignment file\&.
.RE
.PP
\fB\-helixgap=\fR\fB\fIn\fR\fR
.RS 4
-Gap penalty for helix core residues\.
+Gap penalty for helix core residues\&.
.RE
.PP
\fB\-strandgap=\fR\fB\fIn\fR\fR
.RS 4
-Gap penalty for strand core residues\.
+Gap penalty for strand core residues\&.
.RE
.PP
\fBloopgap=\fR\fB\fIn\fR\fR
.RS 4
-Gap penalty for loop regions\.
+Gap penalty for loop regions\&.
.RE
.PP
\fB\-terminalgap=\fR\fB\fIn\fR\fR
.RS 4
-Gap penalty for structure termini\.
+Gap penalty for structure termini\&.
.RE
.PP
\fB\-helixendin=\fR\fB\fIn\fR\fR
.RS 4
-Number of residues inside helix to be treated as terminal\.
+Number of residues inside helix to be treated as terminal\&.
.RE
.PP
\fB\-helixendout=\fR\fB\fIn\fR\fR
.RS 4
-Number of residues outside helix to be treated as terminal\.
+Number of residues outside helix to be treated as terminal\&.
.RE
.PP
\fB\-strandendin=\fR\fB\fIn\fR\fR
.RS 4
-Number of residues inside strand to be treated as terminal\.
+Number of residues inside strand to be treated as terminal\&.
.RE
.PP
\fB\-strandendout=\fR\fB\fIn\fR\fR
.RS 4
-Number of residues outside strand to be treated as terminal\.
+Number of residues outside strand to be treated as terminal\&.
.RE
.RE
.sp
@@ -462,117 +462,117 @@
.PP
\fB\-seed=\fR\fB\fIn\fR\fR
.RS 4
-Seed number for bootstraps\.
+Seed number for bootstraps\&.
.RE
.PP
\fB\-kimura\fR
.RS 4
-Use Kimura\'s correction\.
+Use Kimura\'s correction\&.
.RE
.PP
\fB\-tossgaps\fR
.RS 4
-Ignore positions with gaps\.
+Ignore positions with gaps\&.
.RE
.PP
\fB\-bootlabels=\fR\fB\fInode\fR\fR
.RS 4
-Position of bootstrap values in tree display\.
+Position of bootstrap values in tree display\&.
.RE
.PP
\fB\-clustering=\fR
.RS 4
-NJ or UPGMA\.
+NJ or UPGMA\&.
.RE
.RE
.SH "BUGS"
.PP
The Clustal bug tracking system can be found at
-\fI\%http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal\fR\.
+\fI\%http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal\fR\&.
.SH "SEE ALSO"
.PP
-\fBclustalx\fR(1)\.
+\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]
-Bioinformatics, 23, 2947\-2948\.
+\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]
+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]
-Nucleic Acids Res\., 31, 3497\-3500\.
+\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]
+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\.
+\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\&.
.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]
-Nucleic Acids Res\., 25, 4876\-4882\.
+\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]
+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]
-Methods Enzymol\., 266, 383\-402\.
+\h'-04'\(bu\h'+03'Higgins DG, Thompson JD, Gibson TJ\&. (1996)\&.
+\fIUsing CLUSTAL for multiple sequence alignments\&.\fR\&[5]
+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]
-Nucleic Acids Res\., 22, 4673\-4680\.
+\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]
+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]
-Methods Mol Biol\., 25, 307\-318
+\h'-04'\(bu\h'+03'Higgins DG\&. (1994)\&.
+\fICLUSTAL V: multiple alignment of DNA and protein sequences\&.\fR\&[7]
+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]
-Comput\. Appl\. Biosci\., 8, 189\-191\.
+\h'-04'\(bu\h'+03'Higgins DG, Bleasby AJ, Fuchs R\&. (1992)\&.
+\fICLUSTAL V: improved software for multiple sequence alignment\&.\fR\&[8]
+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]
-Comput\. Appl\. Biosci\., 5, 151\-153\.
+\h'-04'\(bu\h'+03'Higgins,D\&.G\&. and Sharp,P\&.M\&. (1989)\&.
+\fIFast and sensitive multiple sequence alignments on a microcomputer\&.\fR\&[9]
+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]
-Gene, 73, 237\-244\.
+\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]
+Gene, 73, 237\-244\&.
.RE
.SH "AUTHORS"
.PP
\fBDes Higgins\fR
.sp -1n
.IP "" 4
-Copyright holder for Clustal\.
+Copyright holder for Clustal\&.
.PP
\fBJulie Thompson\fR
.sp -1n
.IP "" 4
-Copyright holder for Clustal\.
+Copyright holder for Clustal\&.
.PP
\fBToby Gibson\fR
.sp -1n
.IP "" 4
-Copyright holder for Clustal\.
+Copyright holder for Clustal\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Prepared this manpage in DocBook XML for the Debian distribution\.
+Prepared this manpage in DocBook XML for the Debian distribution\&.
.SH "COPYRIGHT"
Copyright \(co 1988\(en2008 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
.br
@@ -582,21 +582,21 @@
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\.
+\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\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at
-<gibson at embl\.de>
+<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>
-where they will be considered for inclusion in future releases\.
+<clustalw at ucd\&.ie>
+where they will be considered for inclusion in future releases\&.
.RE
.PP
-This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\.
+This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
.sp
.SH "NOTES"
.IP " 1." 4
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-04-30 12:15:50 UTC (rev 1817)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-05-01 01:32:52 UTC (rev 1818)
@@ -16,9 +16,9 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "2.0.5">
+ <!ENTITY dhrelease "2.0.6">
<!ENTITY dhtitle "Clustal Manual">
<!ENTITY dhucpackage "CLUSTALW">
<!ENTITY dhpackage "clustalw">
Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright 2008-04-30 12:15:50 UTC (rev 1817)
+++ trunk/packages/clustalw/trunk/debian/copyright 2008-05-01 01:32:52 UTC (rev 1818)
@@ -15,7 +15,7 @@
© 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 <charles-debian-nospam at plessy.org>
+ © 2007-2008 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
@@ -24,7 +24,7 @@
of Charles Plessy and Steffen Möller can be treated as if it were public domain.
Files: debian/clustalw.1.xml, debian/clustalw.1
-Copyright: © 2008 Charles Plessy <charles-debian-nospam at plessy.org>
+Copyright: © 2008 Charles Plessy <plessy at debian.org>
Licence: Public Domain
The manual page and its XML source can be used, modified, and
redistributed as if it were in public domain.
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