debian/0000755000000000000000000000000012241142035007160 5ustar debian/control0000644000000000000000000000173112241140445010570 0ustar Source: dialign Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/dialign/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/dialign/trunk/ Homepage: http://dialign.gobics.de/ Package: dialign Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Segment-based multiple sequence alignment DIALIGN2 is a command line tool to perform multiple alignment of protein or DNA sequences. It constructs alignments from gapfree pairs of similar segments of the sequences. This scoring scheme for alignments is the basic difference between DIALIGN and other global or local alignment methods. Note that DIALIGN does not employ any kind of gap penalty. debian/install0000644000000000000000000000007111110210453010541 0ustar src/dialign2-2 usr/bin/ dialign2_dir/* usr/share/dialign debian/rules0000755000000000000000000000026212241140352010240 0ustar #!/usr/bin/make -f %: dh $@ override_dh_clean: find src/ -name '*.o' -delete dh_clean src/dialign2-2 override_dh_auto_build: ## CFLAGS = -c -I$ -DCONS -O2 $(MAKE) -C src debian/manpages0000644000000000000000000000002411110210453010664 0ustar debian/dialign2-2.1 debian/watch0000644000000000000000000000021711110210453010203 0ustar version=3 # we use the linux binary package just to get the latest version http://dialign.gobics.de/download/dialign-(.*)-linux\.i586\.tar\.gz debian/upstream0000644000000000000000000000104512214301177010747 0ustar Name: DIALIGN Homepage: http://dialign.gobics.de/ Reference: Author: Burkhard Morgenstern Title: > DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment Journal: Bioinformatics Volume: 15 Number: 3 Pages: 211-218 Year: 1999 DOI: 10.1093/bioinformatics/15.3.211 PMID: 10222408 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/3/211 Eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/15/3/211.pdf Watch: http://dialign.gobics.de/download/dialign-(.*)-linux\.i586\.tar\.gz debian/copyright0000644000000000000000000000304612241141322011114 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Dialign Upstream-Author: Burkhard Morgenstern and Said Abdeddaim Source: http://dialign.gobics.de/download/dialign_package.tgz Files: * Copyright: © 1999 Burkhard Morgenstern License: LGPL-2.1+ License: LGPL-2.1+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA 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 License: LGPL-2.1+ Files: debian/* Copyright: © 2006-2008 Charles Plessy © 2008 Nelson A. de Oliveira © 2008 David Paleino © 2011-2013 Andreas Tille License: PD The packaging work is in the public domain unless stated otherwise. debian/source/0000755000000000000000000000000011514041433010462 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/dialign2-2.10000644000000000000000000002370711110210453011075 0ustar .\" Title: DIALIGN .\" Author: Burkhard Morgenstern .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: avril 9, 2006 .\" Manual: User Manual .\" Source: dialign2-2 2.2.1 .\" .TH "DIALIGN" "1" "avril 9, 2006" "dialign2-2 2.2.1" "User Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" 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)\&. .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\&. .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\&. .RE .sp .RS 4 \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\&. .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)\&. .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! .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! .RE .PP \fB\-anc\fR .RS 4 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\&. .RE .PP \fB\-cw\fR .RS 4 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\&. .RE .PP \fB\-fa\fR .RS 4 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\&. .RE .PP \fB\-fn \fR\fB\fIout_file\fR\fR .RS 4 Output files are named \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\&. .RE .PP \fB\-fsm\fR .RS 4 Creates file \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\&. .RE .PP \fB\-lgs\fR .RS 4 `Long genomic sequences\' \- combines the following options: \fB\-ma\fR, \fB\-thr \fR\fB\fI2\fR\fR, \fB\-lmax \fR\fB\fI30\fR\fR, \fB\-smin \fR\fB\fI8\fR\fR, \fB\-nta\fR, \fB\-ff\fR, \fB\-fop\fR, \fB\-ff\fR, \fB\-cs\fR, \fB\-ds\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\&. .RE .PP \fB\-lmax \fR\fB\fIx\fR\fR .RS 4 Maximum fragment length = \fIx\fR (default: \fIx\fR = 40 or \fIx\fR = 120 for `translated\' fragments)\&. Shorter \fIx\fR 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\&. .RE .PP \fB\-ma\fR .RS 4 `mixed alignments\' consisting of P\-fragments and N\-fragments if nucleic acid sequences are aligned\&. .RE .PP \fB\-mask\fR .RS 4 Residues not belonging to selected fragments are replaced by `*\' characters in output alignment (rather than being printed in lower\-case characters) .RE .PP \fB\-mat\fR .RS 4 Creates file \fI*mat\fR 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\&. .RE .PP \fB\-max_link\fR .RS 4 "Maximum linkage" clustering used to construct sequence tree (instead of UPGMA)\&. .RE .PP \fB\-min_link\fR .RS 4 "Minimum linkage" clustering used\&. .RE .PP \fB\-mot\fR .RS 4 "Motif" option\&. .RE .PP \fB\-msf\fR .RS 4 Separate output file in MSF format\&. .RE .PP \fB\-n\fR .RS 4 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\'\&. .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 \fB\-ff\fR, \fB\-fop\fR, \fB\-fsm\fR or \fB\-lo\fR\&. .RE .PP \fB\-o\fR .RS 4 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\&. .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\&. .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\&. .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\&. .RE .PP \fB\-stdo\fR .RS 4 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)\&. .RE .PP \fB\-thr \fR\fB\fIx\fR\fR .RS 4 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\&. .RE .PP 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!)\&. .SH "SEE ALSO" .PP The full documentation is in \fI/usr/share/doc/dialign/\fR\&. .PP The website of dialign: http://dialign\&.gobics\&.de/ .PP DIALIGN2 has been re\-implemented in \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\&. .SH "FILES" .PP DIALIGN2 needs the files \fItp400_dna\fR, \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\&. .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\&. .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\&. .SH "AUTHORS" .PP \fBBurkhard Morgenstern\fR <\&bmorgen@gwdg\&.de\&> .sp -1n .IP "" 4 Author of DIALIGN .PP \fBSaid Abdeddaim\fR .sp -1n .IP "" 4 Author of DIALIGN .PP \fBCharles Plessy\fR <\&plessy@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\&. .PP This manual page was adapted from the DIALIGN manual by Charles Plessy 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\&. .PP 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 Copyright \(co 2006, 2007, 2008 Charles Plessy (for this manpage) .br debian/README.Debian0000644000000000000000000000062712241140512011224 0ustar dialign for Debian ------------------ In order to make dialign work 'out of the box', I hard-coded the path of the substitution matrices to /usr/share/dialign, where the package installs them. Hence, it is not necessary to set the DIALIGN2_DIR environment variable. Setting it overrides the default path I hard-coded. -- Charles Plessy , Sun, 9 Apr 2006 23:53:26 +0900 debian/changelog0000644000000000000000000000572712241142035011045 0ustar dialign (2.2.1-6) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: Took over more detailed field from tasks file; moved DOI+PMID to References * debian/control: - cme fix dpkg-control - debhelper 9 - remove Build-Depends from quilt * debian/copyright: DEP5 * debian/patches/hardening.patch: Propagate hardening options -- Andreas Tille Thu, 14 Nov 2013 13:23:16 +0100 dialign (2.2.1-5) unstable; urgency=low * Fix FTBFS which is caused by cdbs which is abandoning DEB_OPT_FLAG Just switch to dh Closes: #618057 * Debhelper 8 -- Andreas Tille Sun, 13 Mar 2011 18:36:43 +0100 dialign (2.2.1-4) unstable; urgency=low [ David Paleino ] * Removed myself from Uploaders [ Charles Plessy ] * Documented information in ‘debian/upstream-metadata.yaml’. * Removed mention of the bibliographic reference in ‘debian/control’. [ Andreas Tille ] * debian/control: - Standards-Version: 3.9.1 (no changes needed) - Debhelper 7 - s/dpatch/quilt/ - spelling of Debian Med * debian/patches: converted to quilt * debian/source/format: 3.0 (quilt) * debian/rules: s/dpatch/patchsys-quilt/ -- Andreas Tille Fri, 14 Jan 2011 13:28:33 +0100 dialign (2.2.1-3) unstable; urgency=low * Changed the doc-base section according to the new policy. * Updated my email address. (debian/control, debian/copyright, debian/dialign2-2.1*) -- Charles Plessy Sat, 17 May 2008 18:10:28 +0900 dialign (2.2.1-2) unstable; urgency=low [ Charles Plessy ] * debian/control: - Added URIs to subersion repository. - Moved the Homepage: field out from the package's description. - Added cdbs to the build-dependencies. * debian/rules: - Rewrote for CDBS. * Debian menu transition: - Updated debian/dialign.doc-base. * debian/dialign2-2.1.xml - Corrected typo and grammar in the manpage. - Fixed the auto-generated AUTHORS field. * debian/copyright: - Converted to machine-readable format. - Added Nelson and David there. [ Nelson A. de Oliveira ] * Added watch file. (Closes: #449953) [ David Paleino ] * debian/dialign2-2.1 added - the manpage is now statically built. This saves buildd time and B-D space. * debian/control: - added myself to Uploaders - updated B-D (see above) - moved XS-Vcs-* fields to Vcs-* * Updated to Standards-Version 3.7.3 (no changes needed) [ Andreas Tille ] * Added myself to Uploaders -- Andreas Tille Mon, 17 Mar 2008 09:33:54 +0100 dialign (2.2.1-1) unstable; urgency=low * New upstream release. -- Charles Plessy Mon, 12 Jun 2006 22:01:59 +0900 dialign (2.1.1-1) unstable; urgency=low * Initial release Closes: #361682 -- Charles Plessy Sun, 9 Apr 2006 23:53:26 +0900 debian/patches/0000755000000000000000000000000012241141546010615 5ustar debian/patches/hardening.patch0000644000000000000000000000101212241141546013567 0ustar Author: Andreas Tille LastChanged: Thu, 14 Nov 2013 13:23:16 +0100 Description: Propagate hardening options --- a/src/makefile +++ b/src/makefile @@ -11,7 +11,7 @@ CC = gcc -CFLAGS = -c -O -I$ -DCONS +CFLAGS += -c -O -I$ -DCONS #CFLAGS = -g -c -I$ -DCONS LIBS = -lm # @@ -23,7 +23,7 @@ OBJS = dialign.o functions.o para.o \ # dialign2-2: $(OBJS) - $(CC) $(OBJS) $(LIBS) -o dialign2-2 + $(CC) $(OBJS) $(LIBS) -o dialign2-2 $(LDFLAGS) # $(CC) -g $(OBJS) $(LIBS) -o dialign2-2_db # # debian/patches/20_no_DIALIGN2_DIR.patch0000644000000000000000000000216411514041223014456 0ustar Author: Charles Plessy License: public domain. Description: Gives a default value to par_file so that the environment variable DIALIGN2_DIR is optional --- dialign-2.2.1.orig/src/dialign.c +++ dialign-2.2.1/src/dialign.c @@ -296,10 +296,13 @@ if ((par_file = getenv(dialign_dir)) == NULL) { - printf("\n \n \n Please set the environmentvariable DIALIGN2_DIR \n"); - printf(" as described in the README file \n"); - exit(1); - } + par_file = "/usr/share/dialign/" ; /* Default value for Debian, makes the environment variable optional */ + +/* printf("\n \n \n Please set the environmentvariable DIALIGN2_DIR \n"); + * printf(" as described in the README file \n"); + * exit(1); + */ + } argnum = argc; @@ -523,6 +526,7 @@ printf(" to a directory containing the files \n\n"); printf(" BLOSUM \n tp400_dna\n tp400_prot \n tp400_trans \n\n" ); printf(" These files should be contained in the DIALIGN package \n\n\n" ) ; + printf(" See /usr/share/doc/dialign/README.Debian for more details \n" ) ; exit(1) ; debian/patches/series0000644000000000000000000000007412241141416012027 0ustar 20_no_DIALIGN2_DIR.patch 30_local_doc.patch hardening.patch debian/patches/30_local_doc.patch0000644000000000000000000000162211514041131014047 0ustar Author: Charles Plessy License: public domain. Description: Mentions the man page and /usr/share/doc/dialign when it is invoked without arguments --- dialign-2.2.1.orig/src/dialign.c +++ dialign-2.2.1/src/dialign.c @@ -320,7 +320,7 @@ printf(" -lgs long genomic sequences: Both nucleotide and peptide\n"); printf(" similarities calculated \n\n"); printf(" Many more options are available, please consult the \n"); - printf(" DIALIGN USER_GUIDE that should come with the DIALIGN package.\n"); + printf(" DIALIGN USER_GUIDE in /usr/share/doc/dialign/, or the manpage.\n"); printf(" For more information on DIALIGN, please visit the DIALIGN\n"); printf(" home page at BiBiServ (Bielefeld Bioinformatic Server): \n\n") ; printf(" http://bibiserv.techfak.uni-bielefeld.de/dialign/ \n\n"); debian/dialign.doc-base0000644000000000000000000000032311110210453012156 0ustar Document: dialign Title: Dialign User Manual Author: Burkhard Morgenstern Abstract: This manual describes how to use dialign. Section: Science/Biology Format: text Files: /usr/share/doc/dialign/USER_GUIDE.gz debian/compat0000644000000000000000000000000212241140357010363 0ustar 9 debian/dialign2-2.1.xml0000644000000000000000000004235311110210453011672 0ustar Charles"> Plessy"> avril 9, 2006"> 1"> plessy@debian.org"> DIALIGN"> Debian"> GNU"> GPL"> ]> &dhtitle; &dhpackage; &dhrelease; Burkhard Morgenstern Author of DIALIGN
bmorgen@gwdg.de
Said Abdeddaim Author of DIALIGN &dhfirstname; &dhsurname; Wrote this manpage
&dhemail;
 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. This manual page was adapted from the DIALIGN manual by &dhusername; &dhemail; 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. On Debian systems, the complete text of the GNU Lesser General Public License can be found in /usr/share/common-licenses/LGPL. 1999 Burkhard Morgenstern (for DIALIGN) 2006 2007 2008 &dhusername; (for this manpage) &dhdate; &dhucpackage; &dhsection; &dhpackage; Multiple alignment program using the segment-to-segment approach dialign2-2 options seq_file seq_file is the name of the input sequence file; this must be a multiple FASTA file (all sequences in one file). DESCRIPTION &dhpackage; 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. By default, DIALIGN creates a single file containing An alignment of the input sequences in DIALIGN format. The same alignment in FASTA format. 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. The format of the output files is documented in /usr/share/doc/dialign/USER_GUIDE.gz. The FASTA, CLUSTALW and MSF output formats are optionally available (see OPTIONS). OPTIONS Creates additional output file "*.afc" containing data of all fragments considered for alignment. WARNING: this file can be HUGE! Like "" but verbose: fragments are explicitly printed. WARNING: this file can be EVEN BIGGER! Anchored alignment. Requires a file seq_file.anc containing anchor points. If segments are translated, not only the `Watson strand' but also the `Crick strand' is looked at. Additional output file in CLUSTAL W format. `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. Additional output file in FASTA format. Creates file *.frg containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignment. Output files are named out_file.extension. Creates file *.fop containing coordinates of all fragments that are part of the respective pairwise alignments. Creates file *.fsm containing coordinates of all fragments that are part of the final alignment 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. `Long genomic sequences' - combines the following options: , , , , , , , , , , . Like "" 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. Maximum fragment length = x (default: x = 40 or x = 120 for `translated' fragments). Shorter x speeds up the program but may affect alignment quality. (Long Output) Additional file *.log with information abut fragments selected for pairwise alignment and about consistency in multi-alignment proceedure. `mixed alignments' consisting of P-fragments and N-fragments if nucleic acid sequences are aligned. Residues not belonging to selected fragments are replaced by `*' characters in output alignment (rather than being printed in lower-case characters) Creates file *mat with substitution counts derived from the fragments that have been selected for alignment. Like "-mat" but only fragments with weight score > t are considered. "Maximum linkage" clustering used to construct sequence tree (instead of UPGMA). "Minimum linkage" clustering used. "Motif" option. Separate output file in MSF format. Input sequences are nucleic acid sequences. No translation of fragments. Input sequences are nucleic acid sequences and `nucleic acid segments' are translated to `peptide segments'. `No textual alignment'. Textual alignment suppressed. This option makes sense if other output files are of intrest -- e.g. the fragment files created with , , or . Fast version, resulting alignments may be slightly different. 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. "Print status". Creates and updates a file *.sta 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. 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. Maximum number of `*' characters indicating degree of local similarity among sequences. By default, no stars are used but numbers between 0 and 9, instead. Results written to standard output. Standard textual alignment printed (overrides suppression of textual alignments in special options, e.g. -lgs). Threshold T = x. "Exclude fragments". List of fragments can be specified that are NOT considered for pairwise alignment. General remark: If contradictory options are used, subsequent options override previous ones, e.g.: dialign2-2 -nt -n seq_file runs the program with the "-n" option (no translation!), while dialign2-2 -n -nt seq_file runs it with the "-nt" option (translation!). SEE ALSO The full documentation is in /usr/share/doc/dialign/. The website of dialign: http://dialign.gobics.de/ DIALIGN2 has been re-implemented in dialign-tx1. See http://dialign-tx.gobics.de/ ENVIRONMENT VARIABLES You can create an environment variable `DIALIGN2_DIR' 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. FILES DIALIGN2 needs the files tp400_dna, tp400_prot, tp400_trans and BLOSUM. When DIALIGN is installed from the Debian package, they are stored in /usr/share/dialign/. DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix. In the current version, it is NOT possible to replace BLOSUM62 by other similarity matrices. REFERENCE 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. debian/docs0000644000000000000000000000001311110210453010017 0ustar USER_GUIDE