NAME¶
dialign2-2 - Multiple alignment program using the
segment-to-segment approach
SYNOPSIS¶
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.
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
Creates 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!).
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)
