belvu(1) View multiple alignments in good-looking colours.


belvu [options] <multiple_alignment>|- [X options]
<multiple_alignment>|- = alignment file or pipe.


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


-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>.
Remove partial sequences at startup.
Don't write coordinates to saved file.
-z <char>
Separator char between name and coordinates in saved file.
Show alignment annotations on screen (Stockholm format only).
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.
Draw grid line (for debugging).
Start up with uncoloured alignment (faster).
Show this help.
Show version info.
Some X options: -acefont <font> Main font. -font <font> Menu font.


Erik Sonnhammer <[email protected]>


Version 2.16, compiled Aug 18 2009