Provided by: dialign_2.2.1-6_amd64 bug

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!).

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)