---
name: "belvu"
section: "1"
platform: "linux"
package: "belvu"
version: "4.44.1+dfsg-7.1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/belvu"
---

# belvu(1)

View multiple alignments in good-looking colours

## NAME

belvu - View multiple alignments in good-looking colours

## DESCRIPTION

-

  Belvu - View multiple alignments in good-looking colours.

-

  Usage: belvu \[options\] \<multiple\_alignment\>\|-

-

  \<multiple\_alignment\>\|- = alignment file or pipe.

-

  Options:

- **-c**

  Print Conservation table.

- **-l** \<file\>

  Load residue color code file.

- **-L** \<file\>

  Load markup and organism 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.

**-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\>.

- **-G**

  Penalize gaps in pairwise comparisons.

- **-i**

  Ignore gaps in conservation calculation.

- **-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\> 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)

- **-b** \<n\>

  Apply boostrap analysis with \<n\> bootstrap samples

- **-B**

  Print out bootstrap 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.

- **-u**

  Start up with uncoloured alignment (faster).

- **-h**, **--help**

  Show more detailed usage information

- **--compiled**

  Show package compile date

- **--version**

  Show package version number

- **--abbrev-title-on**

  Abbreviate window title prefixes

- **--abbrev-title-off**

  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 \<gb10@sanger.ac.uk\> Based on original code by Erik Sonnhammer \<Erik.Sonnhammer@sbc.su.se\>

-

  Reference: Scoredist: A simple and robust protein sequence distance estimator.

-

  Erik LL Sonnhammer and Volker Hollich. BMC Bioinformatics 6:108 (2005)

-

  See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.

-

  Copyright (c) 2011-2015: Genome Research Ltd. Belvu is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt

- Version 4.44.1

  14:27:56 Oct 19 2017

## AUTHOR

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