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.
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.)
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
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
Print out # bootstrapped trees and exit
(Negative value -> display bootstrap trees on screen)
Read organism info after this label (default OS)
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.
For documentation, see: http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html
Erik Sonnhammer <[email protected]>
Version 2.16, compiled Aug 18 2009