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dialign2-2.1.gz

DIALIGN(1)                   User Manual                  DIALIGN(1)



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)



dialign2-2 2.2.1            avril 9, 2006                 DIALIGN(1)
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