[med-svn] r1883 - trunk/packages/dialign/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Sat May 17 09:12:51 UTC 2008
Author: plessy
Date: 2008-05-17 09:12:51 +0000 (Sat, 17 May 2008)
New Revision: 1883
Removed:
trunk/packages/dialign/trunk/debian/dirs
Modified:
trunk/packages/dialign/trunk/debian/changelog
trunk/packages/dialign/trunk/debian/copyright
trunk/packages/dialign/trunk/debian/dialign2-2.1
trunk/packages/dialign/trunk/debian/dialign2-2.1.xml
Log:
"Updated my email address, updated to latest debian/copyright format."
Modified: trunk/packages/dialign/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign/trunk/debian/changelog 2008-05-17 08:17:38 UTC (rev 1882)
+++ trunk/packages/dialign/trunk/debian/changelog 2008-05-17 09:12:51 UTC (rev 1883)
@@ -1,9 +1,10 @@
-dialign (2.2.1-3) UNRELEASED; urgency=low
+dialign (2.2.1-3) unstable; urgency=low
* Changed the doc-base section according to the new policy.
- * Updated my email address.
+ * Updated my email address. (debian/control, debian/copyright,
+ debian/dialign2-2.1*)
- -- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 16:58:01 +0900
+ -- Charles Plessy <plessy at debian.org> Sat, 17 May 2008 18:10:28 +0900
dialign (2.2.1-2) unstable; urgency=low
Modified: trunk/packages/dialign/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign/trunk/debian/copyright 2008-05-17 08:17:38 UTC (rev 1882)
+++ trunk/packages/dialign/trunk/debian/copyright 2008-05-17 09:12:51 UTC (rev 1883)
@@ -1,20 +1,9 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Charles Plessy <charles-debian-nospam at plessy.org>
-X-Debianized-Date: Sun, 9 Apr 2006.
-X-Source-Downloaded-From: http://dialign.gobics.de/download/dialign_package.tgz
-X-Upstream-Author: Burkhard Morgenstern and Said Abdeddaim
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: Charles Plessy <plessy at debian.org>
+Debianized-Date: Sun, 9 Apr 2006 23:53:26 +0900
+Original-Source-Location: http://dialign.gobics.de/download/dialign_package.tgz
+Upstream-Author: Burkhard Morgenstern and Said Abdeddaim
-Files: debian/dialign2-2.1*
-Copyright: © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
-License: Same as DIALIGN itself.
-
-Files: debian/*
-Copyright: © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
- © 2008 Nelson A. de Oliveira <naoliv at debian.org>
- © 2008 David Paleino <d.paleino at gmail.com>
-License: PD
- The packaging work is in the public domain unless stated otherwise.
-
Files: *
Copyright: © 1999 Burkhard Morgenstern
License: LGPL-2.1+
@@ -33,3 +22,15 @@
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
X-Comment: On Debian systems, the complete text of the GNU Lesser General
Public License can be found in `/usr/share/common-licenses/LGPL'.
+
+Files: debian/dialign2-2.1*
+Copyright: © 2006-2008 Charles Plessy <plessy at debian.org>
+License: Same as DIALIGN itself.
+ (see above)
+
+Files: debian/*
+Copyright: © 2006-2008 Charles Plessy <plessy at debian.org>
+ © 2008 Nelson A. de Oliveira <naoliv at debian.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
Modified: trunk/packages/dialign/trunk/debian/dialign2-2.1
===================================================================
--- trunk/packages/dialign/trunk/debian/dialign2-2.1 2008-05-17 08:17:38 UTC (rev 1882)
+++ trunk/packages/dialign/trunk/debian/dialign2-2.1 2008-05-17 09:12:51 UTC (rev 1883)
@@ -11,105 +11,105 @@
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dialign2-2 - Multiple alignment program using the segment-to-segment approach
+dialign2-2 \- Multiple alignment program using the segment-to-segment approach
.SH "SYNOPSIS"
.HP 11
\fBdialign2\-2\fR [options] [seq_file]
.PP
\fIseq_file\fR
-is the name of the input sequence file; this must be a multiple FASTA file (all sequences in one file)\.
+is the name of the input sequence file; this must be a multiple FASTA file (all sequences in one file)\&.
.SH "DESCRIPTION"
.PP
\fBdialign2\-2\fR
-is a program that constructs alignments from gapfree pairs of similar segments of the sequences\. If (possibly) coding nucleic acid sequences are to be aligned, DIALIGN optionally translates the compared `nucleic acid segments\' to `peptide segments\' according to the genetic code \-\- without presupposing any of the three possible reading frames, so all combinations of reading frames get checked for significant similarity\.
+is a program that constructs alignments from gapfree pairs of similar segments of the sequences\&. If (possibly) coding nucleic acid sequences are to be aligned, DIALIGN optionally translates the compared `nucleic acid segments\' to `peptide segments\' according to the genetic code \-\- without presupposing any of the three possible reading frames, so all combinations of reading frames get checked for significant similarity\&.
.PP
By default, DIALIGN creates a single file containing
.sp
.RS 4
-\h'-04'\(bu\h'+03'An alignment of the input sequences in DIALIGN format\.
+\h'-04'\(bu\h'+03'An alignment of the input sequences in DIALIGN format\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'The same alignment in FASTA format\.
+\h'-04'\(bu\h'+03'The same alignment in FASTA format\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'A sequence tree in PHYLIP format\. This tree is constructed by applying the UPGMA clustering method to the DIALIGN similarity scores\. It roughly reflects the different degrees of similarity among sequences\. For detailed phylogenetic analysis, we recommend the usual methods for phylogenetic reconstruction\.
+\h'-04'\(bu\h'+03'A sequence tree in PHYLIP format\&. This tree is constructed by applying the UPGMA clustering method to the DIALIGN similarity scores\&. It roughly reflects the different degrees of similarity among sequences\&. For detailed phylogenetic analysis, we recommend the usual methods for phylogenetic reconstruction\&.
.RE
.sp
.RE
.PP
The format of the output files is documented in
-\fI/usr/share/doc/dialign/USER_GUIDE\.gz\fR\. The FASTA, CLUSTALW and MSF output formats are optionally available (see OPTIONS)\.
+\fI/usr/share/doc/dialign/USER_GUIDE\&.gz\fR\&. The FASTA, CLUSTALW and MSF output formats are optionally available (see OPTIONS)\&.
.SH "OPTIONS"
.PP
\fB\-afc\fR
.RS 4
-Creates additional output file "*\.afc" containing data of all fragments considered for alignment\. WARNING: this file can be HUGE!
+Creates additional output file "*\&.afc" containing data of all fragments considered for alignment\&. WARNING: this file can be HUGE!
.RE
.PP
\fB\-afc_v\fR
.RS 4
-Like "\fB\-afc\fR" but verbose: fragments are explicitly printed\. WARNING: this file can be EVEN BIGGER!
+Like "\fB\-afc\fR" but verbose: fragments are explicitly printed\&. WARNING: this file can be EVEN BIGGER!
.RE
.PP
\fB\-anc\fR
.RS 4
-Anchored alignment\. Requires a file
-\fIseq_file\.anc\fR
-containing anchor points\.
+Anchored alignment\&. Requires a file
+\fIseq_file\&.anc\fR
+containing anchor points\&.
.RE
.PP
\fB\-cs\fR
.RS 4
-If segments are translated, not only the `Watson strand\' but also the `Crick strand\' is looked at\.
+If segments are translated, not only the `Watson strand\' but also the `Crick strand\' is looked at\&.
.RE
.PP
\fB\-cw\fR
.RS 4
-Additional output file in CLUSTAL W format\.
+Additional output file in CLUSTAL W format\&.
.RE
.PP
\fB\-ds\fR
.RS 4
-`DNA alignment speed up\'\. Non\-translated nucleic acid fragments are taken into account only if they start with at least two matches\. Speeds up DNA alignment at the expense of sensitivity\.
+`DNA alignment speed up\'\&. Non\-translated nucleic acid fragments are taken into account only if they start with at least two matches\&. Speeds up DNA alignment at the expense of sensitivity\&.
.RE
.PP
\fB\-fa\fR
.RS 4
-Additional output file in FASTA format\.
+Additional output file in FASTA format\&.
.RE
.PP
\fB\-ff\fR
.RS 4
Creates file
-\fI*\.frg\fR
-containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignment\.
+\fI*\&.frg\fR
+containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignment\&.
.RE
.PP
\fB\-fn \fR\fB\fIout_file\fR\fR
.RS 4
Output files are named
-\fIout_file\.extension\fR\.
+\fIout_file\&.extension\fR\&.
.RE
.PP
\fB\-fop\fR
.RS 4
Creates file
-\fI*\.fop\fR
-containing coordinates of all fragments that are part of the respective pairwise alignments\.
+\fI*\&.fop\fR
+containing coordinates of all fragments that are part of the respective pairwise alignments\&.
.RE
.PP
\fB\-fsm\fR
.RS 4
Creates file
-\fI*\.fsm\fR
+\fI*\&.fsm\fR
containing coordinates of all fragments that are part of the final alignment
.RE
.PP
\fB\-iw\fR
.RS 4
-Overlap weights switched off (by default, overlap weights are used if up to 35 sequences are aligned)\. This option speeds up the alignment but may lead to reduced alignment quality\.
+Overlap weights switched off (by default, overlap weights are used if up to 35 sequences are aligned)\&. This option speeds up the alignment but may lead to reduced alignment quality\&.
.RE
.PP
\fB\-lgs\fR
@@ -125,12 +125,12 @@
\fB\-ff\fR,
\fB\-cs\fR,
\fB\-ds\fR,
-\fB\-pst\fR\.
+\fB\-pst\fR\&.
.RE
.PP
\fB\-lgs_t\fR
.RS 4
-Like "\fB\-lgs\fR" but with all segment pairs assessed at the peptide level (rather than \'mixed alignments\' as with the "\-lgs" option)\. Therefore faster than \-lgs but not very sensitive for non\-coding regions\.
+Like "\fB\-lgs\fR" but with all segment pairs assessed at the peptide level (rather than \'mixed alignments\' as with the "\-lgs" option)\&. Therefore faster than \-lgs but not very sensitive for non\-coding regions\&.
.RE
.PP
\fB\-lmax \fR\fB\fIx\fR\fR
@@ -141,21 +141,21 @@
\fIx\fR
= 40 or
\fIx\fR
-= 120 for `translated\' fragments)\. Shorter
+= 120 for `translated\' fragments)\&. Shorter
\fIx\fR
-speeds up the program but may affect alignment quality\.
+speeds up the program but may affect alignment quality\&.
.RE
.PP
\fB\-lo\fR
.RS 4
(Long Output) Additional file
-\fI*\.log\fR
-with information abut fragments selected for pairwise alignment and about consistency in multi\-alignment proceedure\.
+\fI*\&.log\fR
+with information abut fragments selected for pairwise alignment and about consistency in multi\-alignment proceedure\&.
.RE
.PP
\fB\-ma\fR
.RS 4
-`mixed alignments\' consisting of P\-fragments and N\-fragments if nucleic acid sequences are aligned\.
+`mixed alignments\' consisting of P\-fragments and N\-fragments if nucleic acid sequences are aligned\&.
.RE
.PP
\fB\-mask\fR
@@ -167,122 +167,122 @@
.RS 4
Creates file
\fI*mat\fR
-with substitution counts derived from the fragments that have been selected for alignment\.
+with substitution counts derived from the fragments that have been selected for alignment\&.
.RE
.PP
\fB\-mat_thr \fR\fB\fIt\fR\fR
.RS 4
Like "\-mat" but only fragments with weight score >
\fIt\fR
-are considered\.
+are considered\&.
.RE
.PP
\fB\-max_link\fR
.RS 4
-"Maximum linkage" clustering used to construct sequence tree (instead of UPGMA)\.
+"Maximum linkage" clustering used to construct sequence tree (instead of UPGMA)\&.
.RE
.PP
\fB\-min_link\fR
.RS 4
-"Minimum linkage" clustering used\.
+"Minimum linkage" clustering used\&.
.RE
.PP
\fB\-mot\fR
.RS 4
-"Motif" option\.
+"Motif" option\&.
.RE
.PP
\fB\-msf\fR
.RS 4
Separate output file in
MSF
-format\.
+format\&.
.RE
.PP
\fB\-n\fR
.RS 4
-Input sequences are nucleic acid sequences\. No translation of fragments\.
+Input sequences are nucleic acid sequences\&. No translation of fragments\&.
.RE
.PP
\fB\-nt\fR
.RS 4
-Input sequences are nucleic acid sequences and `nucleic acid segments\' are translated to `peptide segments\'\.
+Input sequences are nucleic acid sequences and `nucleic acid segments\' are translated to `peptide segments\'\&.
.RE
.PP
\fB\-nta\fR
.RS 4
-`No textual alignment\'\. Textual alignment suppressed\. This option makes sense if other output files are of intrest \-\- e\.g\. the fragment files created with
+`No textual alignment\'\&. Textual alignment suppressed\&. This option makes sense if other output files are of intrest \-\- e\&.g\&. the fragment files created with
\fB\-ff\fR,
\fB\-fop\fR,
\fB\-fsm\fR
or
-\fB\-lo\fR\.
+\fB\-lo\fR\&.
.RE
.PP
\fB\-o\fR
.RS 4
-Fast version, resulting alignments may be slightly different\.
+Fast version, resulting alignments may be slightly different\&.
.RE
.PP
\fB\-ow\fR
.RS 4
-Overlap weights enforced (By default, overlap weights are used only if up to 35 sequences are aligned since calculating overlap weights is time consuming)\. Warning: overlap weights generally improve alignment quality but the running time increases in the order O(n^4) with the number of sequences\. This is why, by default, overlap weights are used only for sequence sets with < 36 sequences\.
+Overlap weights enforced (By default, overlap weights are used only if up to 35 sequences are aligned since calculating overlap weights is time consuming)\&. Warning: overlap weights generally improve alignment quality but the running time increases in the order O(n^4) with the number of sequences\&. This is why, by default, overlap weights are used only for sequence sets with < 36 sequences\&.
.RE
.PP
\fB\-pst\fR
.RS 4
-"Print status"\. Creates and updates a file
-\fI*\.sta\fR
-with information about the current status of the program run\. This option is recommended if large data sets are aligned since it allows the user to estimate the remaining running time\.
+"Print status"\&. Creates and updates a file
+\fI*\&.sta\fR
+with information about the current status of the program run\&. This option is recommended if large data sets are aligned since it allows the user to estimate the remaining running time\&.
.RE
.PP
\fB\-smin \fR\fB\fIx\fR\fR
.RS 4
-Minimum similarity value for first residue pair (or codon pair) in fragments\. Speeds up protein alignment or alignment of translated DNA fragments at the expense of sensitivity\.
+Minimum similarity value for first residue pair (or codon pair) in fragments\&. Speeds up protein alignment or alignment of translated DNA fragments at the expense of sensitivity\&.
.RE
.PP
\fB\-stars \fR\fB\fIx\fR\fR
.RS 4
-Maximum number of `*\' characters indicating degree of local similarity among sequences\. By default, no stars are used but numbers between 0 and 9, instead\.
+Maximum number of `*\' characters indicating degree of local similarity among sequences\&. By default, no stars are used but numbers between 0 and 9, instead\&.
.RE
.PP
\fB\-stdo\fR
.RS 4
-Results written to standard output\.
+Results written to standard output\&.
.RE
.PP
\fB\-ta\fR
.RS 4
-Standard textual alignment printed (overrides suppression of textual alignments in special options, e\.g\. \-lgs)\.
+Standard textual alignment printed (overrides suppression of textual alignments in special options, e\&.g\&. \-lgs)\&.
.RE
.PP
\fB\-thr \fR\fB\fIx\fR\fR
.RS 4
-Threshold T = x\.
+Threshold T = x\&.
.RE
.PP
\fB\-xfr\fR
.RS 4
-"Exclude fragments"\. List of fragments can be specified that are NOT considered for pairwise alignment\.
+"Exclude fragments"\&. List of fragments can be specified that are NOT considered for pairwise alignment\&.
.RE
.PP
-General remark: If contradictory options are used, subsequent options override previous ones, e\.g\.:
+General remark: If contradictory options are used, subsequent options override previous ones, e\&.g\&.:
dialign2\-2 \-nt \-n \fIseq_file\fR
runs the program with the "\-n" option (no translation!), while
dialign2\-2 \-n \-nt \fIseq_file\fR
-runs it with the "\-nt" option (translation!)\.
+runs it with the "\-nt" option (translation!)\&.
.SH "SEE ALSO"
.PP
The full documentation is in
-\fI/usr/share/doc/dialign/\fR\.
+\fI/usr/share/doc/dialign/\fR\&.
.PP
-The website of dialign: http://dialign\.gobics\.de/
+The website of dialign: http://dialign\&.gobics\&.de/
.PP
DIALIGN2 has been re\-implemented in
-\fBdialign-t\fR(1)\. See http://dialign\-t\.gobics\.de/
+\fBdialign-tx\fR(1)\&. See http://dialign\-tx\&.gobics\&.de/
.SH "ENVIRONMENT VARIABLES"
.PP
-You can create an environment variable `\fBDIALIGN2_DIR\fR\' pointing to a directory where the substitution matrices are (see FILES)\. When installed from the Debian package, it is not necessary to set this environnement variable to run DIALIGN\.
+You can create an environment variable `\fBDIALIGN2_DIR\fR\' pointing to a directory where the substitution matrices are (see FILES)\&. When installed from the Debian package, it is not necessary to set this environnement variable to run DIALIGN\&.
.SH "FILES"
.PP
DIALIGN2 needs the files
@@ -290,16 +290,16 @@
\fItp400_prot\fR,
\fItp400_trans\fR
and
-\fIBLOSUM\fR\. When DIALIGN is installed from the Debian package, they are stored in
-\fI/usr/share/dialign/\fR\.
+\fIBLOSUM\fR\&. When DIALIGN is installed from the Debian package, they are stored in
+\fI/usr/share/dialign/\fR\&.
.PP
-DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix\. In the current version, it is NOT possible to replace BLOSUM62 by other similarity matrices\.
+DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix\&. In the current version, it is NOT possible to replace BLOSUM62 by other similarity matrices\&.
.SH "REFERENCE"
.PP
-B\. Morgenstern (1999)\. DIALIGN 2: improvement of the segment\-to\-segment approach to multiple sequence alignment\. Bioinformatics 15, 211 \- 218\. Public research assisted by DIALIGN should cite this article\.
+B\&. Morgenstern (1999)\&. DIALIGN 2: improvement of the segment\-to\-segment approach to multiple sequence alignment\&. Bioinformatics 15, 211 \- 218\&. Public research assisted by DIALIGN should cite this article\&.
.SH "AUTHORS"
.PP
-\fBBurkhard Morgenstern\fR <\&bmorgen at gwdg\.de\&>
+\fBBurkhard Morgenstern\fR <\&bmorgen at gwdg\&.de\&>
.sp -1n
.IP "" 4
Author of DIALIGN
@@ -309,21 +309,21 @@
.IP "" 4
Author of DIALIGN
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
Wrote this manpage
.SH "COPYRIGHT"
.PP
-DIALIGN was written by Burkhard Morgenstern and Said Abdeddaim at University of Bielefeld (FSPM and International Graduate School in Bioinformatics and Genome Research), GSF (ISG, IBB, MIPS/IBI), North Carolina State University, Universite de Rouen, MPI fuer Biochemie (Martinsried), University of Goettingen, Institute of Microbiology and Genetics\.
+DIALIGN was written by Burkhard Morgenstern and Said Abdeddaim at University of Bielefeld (FSPM and International Graduate School in Bioinformatics and Genome Research), GSF (ISG, IBB, MIPS/IBI), North Carolina State University, Universite de Rouen, MPI fuer Biochemie (Martinsried), University of Goettingen, Institute of Microbiology and Genetics\&.
.PP
This manual page was adapted from the DIALIGN manual by Charles Plessy
-<charles\-debian\-nospam at plessy\.org>
-for the Debian system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the terms of the
+<plessy at debian\&.org>
+for the Debian system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the terms of the
GNU
-Lesser General Public License, Version 2\.1 any later version published by the Free Software Foundation\.
+Lesser General Public License, Version 2\&.1 any later version published by the Free Software Foundation\&.
.PP
-On Debian systems, the complete text of the GNU Lesser General Public License can be found in /usr/share/common\-licenses/LGPL\.
+On Debian systems, the complete text of the GNU Lesser General Public License can be found in /usr/share/common\-licenses/LGPL\&.
.sp
Copyright \(co 1999 Burkhard Morgenstern (for DIALIGN)
.br
Modified: trunk/packages/dialign/trunk/debian/dialign2-2.1.xml
===================================================================
--- trunk/packages/dialign/trunk/debian/dialign2-2.1.xml 2008-05-17 08:17:38 UTC (rev 1882)
+++ trunk/packages/dialign/trunk/debian/dialign2-2.1.xml 2008-05-17 09:12:51 UTC (rev 1883)
@@ -8,7 +8,7 @@
<!ENTITY dhsurname "<surname>Plessy</surname>">
<!ENTITY dhdate "<date>avril 9, 2006</date>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhemail "<email>plessy at debian.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhucpackage "<refentrytitle>DIALIGN</refentrytitle>">
<!ENTITY dhpackage "dialign2-2">
@@ -429,7 +429,7 @@
<para>The website of dialign: http://dialign.gobics.de/</para>
- <para>DIALIGN2 has been re-implemented in <citerefentry><refentrytitle>dialign-t</refentrytitle><manvolnum>1</manvolnum></citerefentry>. See http://dialign-t.gobics.de/</para>
+ <para>DIALIGN2 has been re-implemented in <citerefentry><refentrytitle>dialign-tx</refentrytitle><manvolnum>1</manvolnum></citerefentry>. See http://dialign-tx.gobics.de/</para>
</refsect1>
Deleted: trunk/packages/dialign/trunk/debian/dirs
===================================================================
--- trunk/packages/dialign/trunk/debian/dirs 2008-05-17 08:17:38 UTC (rev 1882)
+++ trunk/packages/dialign/trunk/debian/dirs 2008-05-17 09:12:51 UTC (rev 1883)
@@ -1,2 +0,0 @@
-usr/bin
-usr/share/dialign
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