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

belvu 2.19                                         August 2009                                          BELVU(1)