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•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.
OPTIONS¶
-afcCreates additional output file
"*.afc" containing data of all fragments considered for alignment.
WARNING: this file can be HUGE!
-afc_v
Like "-afc" but verbose:
fragments are explicitly printed. WARNING: this file can be EVEN BIGGER!
-anc
Anchored alignment. Requires a file
seq_file.anc containing anchor points.
-cs
If segments are translated, not only the
`Watson strand´ but also the `Crick strand´ is looked at.
-cw
Additional output file in CLUSTAL W
format.
-ds
`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.
-fa
Additional output file in FASTA format.
-ff
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.
-fn out_file
Output files are named
out_file.extension.
-fop
Creates file *.fop containing
coordinates of all fragments that are part of the respective pairwise
alignments.
-fsm
Creates file *.fsm containing
coordinates of all fragments that are part of the final alignment
-iw
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.
-lgs
`Long genomic sequences´ - combines the
following options: -ma, -thr 2, -lmax
30, -smin 8, -nta, -ff,
-fop, -ff, -cs, -ds, -pst.
-lgs_t
Like "-lgs" 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.
-lmax x
Maximum fragment length = x (default:
x = 40 or x = 120 for `translated´ fragments). Shorter
x speeds up the program but may affect alignment quality.
-lo
(Long Output) Additional file *.log
with information abut fragments selected for pairwise alignment and about
consistency in multi-alignment proceedure.
-ma
`mixed alignments´ consisting of
P-fragments and N-fragments if nucleic acid sequences are aligned.
-mask
Residues not belonging to selected fragments
are replaced by `*´ characters in output alignment (rather than being
printed in lower-case characters)
-mat
Creates file *mat with substitution
counts derived from the fragments that have been selected for alignment.
-mat_thr t
Like "-mat" but only fragments with
weight score > t are considered.
-max_link
"Maximum linkage" clustering used to
construct sequence tree (instead of UPGMA).
-min_link
"Minimum linkage" clustering
used.
-mot
"Motif" option.
-msf
Separate output file in MSF format.
-n
Input sequences are nucleic acid sequences. No
translation of fragments.
-nt
Input sequences are nucleic acid sequences and
`nucleic acid segments´ are translated to `peptide segments´.
-nta
`No textual alignment´. Textual alignment
suppressed. This option makes sense if other output files are of intrest --
e.g. the fragment files created with -ff, -fop, -fsm or
-lo.
-o
Fast version, resulting alignments may be
slightly different.
-ow
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.
-pst
"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.
-smin x
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.
-stars x
Maximum number of `*´ characters
indicating degree of local similarity among sequences. By default, no stars
are used but numbers between 0 and 9, instead.
-stdo
Results written to standard output.
-ta
Standard textual alignment printed (overrides
suppression of textual alignments in special options, e.g. -lgs).
-thr x
Threshold T = x.
-xfr
"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-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
- Author of DIALIGN
- 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.| avril 9, 2006 | dialign2-2 2.2.1 |