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belvu(1)


NAME

   belvu - View multiple alignments in good-looking colours.

SYNOPSIS

   belvu [options] <multiple_alignment>|- [X options]

          <multiple_alignment>|- = alignment file or pipe.

DESCRIPTION

   Belvu presents multiple sequence alignments in a colourful biologically
   interpretable manner.

OPTIONS

   -c          Print Conservation table.

   -l <file>   Load color code file.

   -L <file>   Load Markup 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.

   -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>.

   -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> Start up with tree calculated by method:

          n  ->  Neighbor-joining  u  -> UPGMA N -> Neighbor-joining, only
          show tree U -> UPGMA, only show tree c -> Don't  color  tree  by
          organism  o  ->  Don't display sequence coordinates in tree s ->
          Use Storm & Sonnhammer distance correction r -> Use  uncorrected
          distances

   -b <#>
          Print out # bootstrapped 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.

   -g     Draw grid line (for debugging).

   -u     Start up with uncoloured alignment (faster).

   -h     Show this help.

   -v     Show version info.

          Some  X  options:  -acefont <font>   Main font.  -font    <font>
          Menu font.

SEE ALSO

   For                         documentation,                         see:
   http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html

AUTHOR

   Erik Sonnhammer <Erik.Sonnhammer@cgb.ki.se>

VERSION

   Version 2.16, compiled Aug 18 2009



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