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       dialign2-2 - Multiple alignment program using the segment-to-segment


       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).


       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

       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).


           Creates additional output file "*.afc" containing data of all
           fragments considered for alignment. WARNING: this file can be HUGE!

           Like "-afc" but verbose: fragments are explicitly printed. WARNING:
           this file can be EVEN BIGGER!

           Anchored alignment. Requires a file seq_file.anc containing anchor

           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.

       -fn out_file
           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: -ma,
           -thr 2, -lmax 30, -smin 8, -nta, -ff, -fop, -ff, -cs, -ds, -pst.

           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

       -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.

           (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.

       -mat_thr t
           Like "-mat" but only fragments with weight score > t are

           "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

           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 -ff, -fop, -fsm or -lo.

           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

           "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.

           Results written to standard output.

           Standard textual alignment printed (overrides suppression of
           textual alignments in special options, e.g. -lgs).

       -thr x
           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!).


       The full documentation is in /usr/share/doc/dialign/.

       The website of dialign:

       DIALIGN2 has been re-implemented in dialign-tx(1). See


       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.


       DIALIGN2 needs the files tp400_dna, tp400_prot, tp400_trans and BLOSUM.
       When DIALIGN is installed from the Debian package, they are stored in

       DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix. In the
       current version, it is NOT possible to replace BLOSUM62 by other
       similarity matrices.


       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.


       Burkhard Morgenstern <>
           Author of DIALIGN

       Said Abdeddaim
           Author of DIALIGN

       Charles Plessy <>
           Wrote this manpage


       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

       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.

       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)