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BELVU(1) User Commands BELVU(1)


belvu - View multiple alignments in good-looking colours


Belvu - View multiple alignments in good-looking colours.
Usage: belvu [options] <multiple_alignment>|-
<multiple_alignment>|- = alignment file or pipe.
Print Conservation table.
Load residue color code file.
Load markup and organism color code file.
Read file with matching sequence segments.
Read alignment in 'raw' format (Name sequence).
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.

-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>.

Penalize gaps in pairwise comparisons.
Ignore gaps in conservation calculation.
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> 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)
Apply boostrap analysis with <n> bootstrap samples
Print out bootstrap trees and exit (Negative value -> display bootstrap trees on screen)
Read organism info after this label (default OS)
Set window title.
Start up with uncoloured alignment (faster).
Show more detailed usage information
Show package compile date
Show package version number
Abbreviate window title prefixes
Do not abbreviate window title prefixes
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 <> Based on original code by Erik Sonnhammer <>
Reference: Scoredist: A simple and robust protein sequence distance estimator.
Erik LL Sonnhammer and Volker Hollich. BMC Bioinformatics 6:108 (2005)
See for more info.
Copyright (c) 2011-2015: Genome Research Ltd. Belvu is distributed under the GNU General Public License; see
14:27:56 Oct 19 2017


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

October 2017 belvu 4.44.1