belvu - 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
Print Conservation table.
<file> Load color code file.
<file> Load Markup color code file.
<file> Read file with matching sequence segments.
Read alignment in 'raw' format (Name sequence).
not parse coordinates when reading alignment.
<format> Write alignment or tree to stdout in this format and
- Valid formats: MSF, Mul(Stockholm), Selex,
- FastaAlign, Fasta, tree.
<cutoff> Make non-redundant to <cutoff> %identity at
<cutoff> Remove columns more gappy than <cutoff>.
<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
- Show alignment annotations on screen (Stockholm format
- 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.
<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
- -b <#>
- Print out # bootstrapped trees and exit
- (Negative value -> display bootstrap trees on
- -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.
For documentation, see: http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html
Erik Sonnhammer <Erik.Sonnhammer@cgb.ki.se>
Version 2.16, compiled Aug 18 2009