NAME

       belvu - View multiple alignments in good-looking colours

DESCRIPTION

              Belvu - View multiple alignments in good-looking colours.

              Usage: belvu [options] <multiple_alignment>|-

              <multiple_alignment>|- = alignment file or pipe.

              Options:

       -c     Print Conservation table.

       -l <file>
              Load residue color code file.

       -L <file>
              Load markup and organism color code file.

       -m <file>
              Read file with matching sequence segments.

       -r     Read alignment in 'raw' format (Name sequence).

       -R     Do not parse coordinates when reading alignment.

       -o <format> Write alignment or tree to stdout in this format and exit.

              Valid formats: MSF, Mul(Stockholm), Selex, FastaAlign, Fasta, tree.

       -X <cutoff> Print UPGMA-based subfamilies at cutoff <cutoff>.

       -n <cutoff> Make non-redundant to <cutoff> %identity at startup.

       -Q <cutoff> Remove columns more gappy than <cutoff>.

       -q <cutoff> Remove sequences more gappy than <cutoff>.

       -G     Penalize gaps in pairwise comparisons.

       -i     Ignore gaps in conservation calculation.

       -P     Remove partial sequences at startup.

       -C     Don't write coordinates to saved file.

       -z <char>
              Separator char between name and coordinates in saved file.

       -a     Show alignment annotations on screen (Stockholm format only).

       -p     Output random model probabilites for HMMER.  (Based on all residues.)

       -S <order>
              Sort sequences in this order.

              a  ->  alphabetically o -> by Swissprot organism, alphabetically s -> by score n ->
              by Neighbor-joining tree u -> by UPGMA tree S -> by similarity to first sequence  i
              -> by identity to first sequence

       -s <file>
              Read in file of scores.

       -T <method> Tree options:

              i  ->  Start up showing tree I -> Start up showing only tree d -> Show distances in
              tree n -> Neighbor-joining u -> UPGMA c -> Don't color tree by organism o ->  Don't
              display  sequence  coordinates  in  tree  b  ->  Use  Scoredist distance correction
              (default) j -> Use Jukes-Cantor  distance  correction  k  ->  Use  Kimura  distance
              correction  s  ->  Use  Storm & Sonnhammer distance correction r -> Use uncorrected
              distances p -> Print distance matrix and exit R -> Read distance matrix instead  of
              alignment

              (only in combination with Tree routines)

       -b <n>
              Apply boostrap analysis with <n> bootstrap samples

       -B     Print  out  bootstrap  trees and exit (Negative value -> display bootstrap trees on
              screen)

       -O <label>
              Read organism info after this label (default OS)

       -t <title>
              Set window title.

       -u     Start up with uncoloured alignment (faster).

       -h, --help
              Show more detailed usage information

       --compiled
              Show package compile date

       --version
              Show package version number

       --abbrev-title-on
              Abbreviate window title prefixes

       --abbrev-title-off
              Do not abbreviate window title prefixes

              setenv BELVU_FETCH to desired sequence fetching program.  setenv BELVU_FONT_SIZE to
              specify  window  font  size.  setenv BELVU_STATUSBAR_SIZE to specify statusbar font
              size (0 => hide statusbar).

       -----

              Written by  Gemma  Barson  <gb10@sanger.ac.uk>  Based  on  original  code  by  Erik
              Sonnhammer <Erik.Sonnhammer@sbc.su.se>

              Reference: Scoredist: A simple and robust protein sequence distance estimator.

              Erik LL Sonnhammer and Volker Hollich.  BMC Bioinformatics 6:108 (2005)

              See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.

              Copyright  (c)  2011-2015: Genome Research Ltd.  Belvu is distributed under the GNU
              General Public License; see http://www.gnu.org/copyleft/gpl.txt

       Version 4.44.1
              14:27:56 Oct 19 2017

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.