
 Belvu - View multiple alignments in pretty colours.

 Usage: belvu [options]  <multiple_alignment>|-

 <multiple_alignment>|- = file or pipe in Stockholm/Selex/MSF/Fasta format (see below).


 Options:

  -c          Print Conservation table.
  -l <file>   Load residue color code file.

              Format: <symbol> <color>
              (Lines starting with # are ignored (comment lines))

              Example of color code file:

                  # Aroma
                  F YELLOW
                  Y YELLOW
                  W YELLOW

                  # Yuck
                  D RED 
                  N GREEN
                  X BLUE

              Available colors:

                    WHITE 
                    BLACK 
                    LIGHTGRAY
                    DARKGRAY
                    RED 
                    GREEN
                    BLUE
                    YELLOW
                    CYAN 
                    MAGENTA
                    LIGHTRED 
                    LIGHTGREEN 
                    LIGHTBLUE
                    DARKRED 
                    DARKGREEN 
                    DARKBLUE
                    PALERED 
                    PALEGREEN 
                    PALEBLUE
                    PALEYELLOW 
                    PALECYAN 
                    PALEMAGENTA
                    BROWN 
                    ORANGE 
                    PALEORANGE
                    PURPLE 
                    VIOLET 
                    PALEVIOLET
                    GRAY 
                    PALEGRAY
                    CERISE 
                    MIDBLUE


  -L <file>  Load markup and organism color code file.
             Colour the markup text by residue or colour organism in tree.

	     Example to set color of letters A and B:
	     A GREEN
	     B YELLOW

	     Example to set color of organism human:
	     #=OS BLUE human


  -m <file>   Read file with matching sequences segments. This is used to
              display a match of  a query sequence to a family.  The format
              of the match is :

              Line 1: Name/start-end score
              Line 2: Query sequence in matching segment, no pads!
              Line 3: Sequence of matching segments (qstart1 qend1 fstart1
              fend2 qstart2 qend2 fstart2 fend2  etc...).

              Example:

              ZK673.9/238-260 21.58
              CPENWVQFTGNGTQYGVCLRGFT
              1 2 1 2  4 7 8 11  

              NOTE: A sometimes easier way of doing this is to concatenate
              the match to the end of the alignment, after a line with
              exactly this string within the quotes: # matchFooter


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

              Example of raw alignment file: 

                  seq1_name MFILKTP
                  seq1_name MYI.RTP

  -R          Do not parse coordinates when reading alignment.
  -o <format> Write alignment or tree to stdout in this format and exit.
                Valid formats: Mul(Stockholm), Selex, MSF, 
                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.A column with scores will
              automatically appear after the coordinates.

              Format: <score> <sequence_id>

              Example of score file:

                  2.78 seq_1/180-206
                  2.78 seq_2/180-206
                  3.79 seq_3/42-94


  -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 this help information
  --compiled  Show package compile date
  --version   Show package version number
 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: Genome Research Ltd.
 Belvu is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt

