debian man page for belvu

BELVU(1)							   User Commands							  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

belvu 2.19							    August 2009 							  BELVU(1)