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 <[email protected]> Based on original code by Erik Sonnhammer <[email protected]>
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.