Man pages sections > man1 > belvu

belvu - View multiple alignments in good-looking colours.

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
August 2009 belvu 2.19