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.

belvu 4.44.1                                      October 2017                                          BELVU(1)