BELVU(1)

🦋 NAME 🦋

belvu — View multiple alignments in good-looking colours 💅✨

🌸 DESCRIPTION 🌸

Okay bestie, listen up: Belvu is here to let you view multiple alignments in good-looking colours. That's the whole gig. It's giving gorgeous, it's giving aligned, periodt. 👑

Here's how you run it:

Usage: belvu [options] <multiple_alignment>|-

And what's that last bit mean?

• <multiple_alignment>|- = alignment file or pipe. Yes, you can pipe it in. The - is the main character here. 🫶

✨ Options ✨

• -c — Print the Conservation table.
• -l <file> — Load a residue color code file. Make it pretty. 🎀
• -L <file> — Load a markup and organism color code file.
• -m <file> — Read a file with matching sequence segments.
• -r — Read the alignment in 'raw' format (Name sequence).
• -R — Do not parse coordinates when reading the alignment.
• -o <format> — Write the 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. Gaps get no mercy. 😤
• -i — Ignore gaps in conservation calculation.
• -P — Remove partial sequences at startup.
• -C — Don't write coordinates to the saved file.
• -z <char> — Separator char between name and coordinates in the 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 a 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). Speed queen. 🏃‍♀️💨
• -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.

Also, the environment variables, bestie — set them like this:

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. Slay, Andreas. 🫶

And that's the whole page, bestie — this was <code>belvu 4.44.1</code>, born <code>October 2017</code>. Go forth and align something gorgeous. 💜✨🎀