table of contents
DIALIGN(1) | User Manual | DIALIGN(1) |
NAME¶
dialign2-2 - Multiple alignment program using the segment-to-segment approachSYNOPSIS¶
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¶
dialign2-2 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
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¶
-afc-afc_v
-anc
-cs
-cw
-ds
-fa
-ff
-fn out_file
-fop
-fsm
-iw
-lgs
-lgs_t
-lmax x
-lo
-ma
-mask
-mat
-mat_thr t
-max_link
-min_link
-mot
-msf
-n
-nt
-nta
-o
-ow
-pst
-smin x
-stars x
-stdo
-ta
-thr x
-xfr
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-tx(1). 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.AUTHORS¶
Burkhard Morgenstern <bmorgen@gwdg.de>- Author of DIALIGN
Said Abdeddaim
- Author of DIALIGN
Charles Plessy <plessy@debian.org>
- Wrote this manpage
COPYRIGHT¶
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 Charles Plessy <plessy@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.
On Debian systems, the complete text of the GNU Lesser General Public License can be found in /usr/share/common-licenses/LGPL.
Copyright © 1999 Burkhard Morgenstern (for DIALIGN)
Copyright © 2006, 2007, 2008 Charles Plessy (for this manpage)
avril 9, 2006 | dialign2-2 2.2.1 |