.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BELVU "1" "October 2017" "belvu 4.44.1" "User Commands"
.SH NAME
belvu \- View multiple alignments in good-looking colours
.SH DESCRIPTION
.IP
Belvu \- View multiple alignments in good\-looking colours.
.IP
Usage: belvu [options] <multiple_alignment>|\-
.IP
<multiple_alignment>|\- = alignment file or pipe.
.IP
Options:
.TP
\fB\-c\fR
Print Conservation table.
.TP
\fB\-l\fR <file>
Load residue color code file.
.TP
\fB\-L\fR <file>
Load markup and organism color code file.
.TP
\fB\-m\fR <file>
Read file with matching sequence segments.
.TP
\fB\-r\fR
Read alignment in 'raw' format (Name sequence).
.TP
\fB\-R\fR
Do not parse coordinates when reading alignment.
.HP
\fB\-o\fR <format> Write alignment or tree to stdout in this format and exit.
.IP
Valid formats: MSF, Mul(Stockholm), Selex,
FastaAlign, Fasta, tree.
.HP
\fB\-X\fR <cutoff> Print UPGMA\-based subfamilies at cutoff <cutoff>.
.HP
\fB\-n\fR <cutoff> Make non\-redundant to <cutoff> %identity at startup.
.HP
\fB\-Q\fR <cutoff> Remove columns more gappy than <cutoff>.
.HP
\fB\-q\fR <cutoff> Remove sequences more gappy than <cutoff>.
.TP
\fB\-G\fR
Penalize gaps in pairwise comparisons.
.TP
\fB\-i\fR
Ignore gaps in conservation calculation.
.TP
\fB\-P\fR
Remove partial sequences at startup.
.TP
\fB\-C\fR
Don't write coordinates to saved file.
.TP
\fB\-z\fR <char>
Separator char between name and coordinates in saved file.
.TP
\fB\-a\fR
Show alignment annotations on screen (Stockholm format only).
.TP
\fB\-p\fR
Output random model probabilites for HMMER.
(Based on all residues.)
.TP
\fB\-S\fR <order>
Sort sequences in this order.
.IP
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
.TP
\fB\-s\fR <file>
Read in file of scores.
.HP
\fB\-T\fR <method> Tree options:
.IP
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
.IP
(only in combination with Tree routines)
.TP
\fB\-b\fR <n>
Apply boostrap analysis with <n> bootstrap samples
.TP
\fB\-B\fR
Print out bootstrap trees and exit
(Negative value \-> display bootstrap trees on screen)
.TP
\fB\-O\fR <label>
Read organism info after this label (default OS)
.TP
\fB\-t\fR <title>
Set window title.
.TP
\fB\-u\fR
Start up with uncoloured alignment (faster).
.TP
\fB\-h\fR, \fB\-\-help\fR
Show more detailed usage information
.TP
\fB\-\-compiled\fR
Show package compile date
.TP
\fB\-\-version\fR
Show package version number
.TP
\fB\-\-abbrev\-title\-on\fR
Abbreviate window title prefixes
.TP
\fB\-\-abbrev\-title\-off\fR
Do not abbreviate window title prefixes
.IP
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).
.PP
\fB\-\-\-\-\-\fR
.IP
Written by Gemma Barson <gb10@sanger.ac.uk>
Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se>
.IP
Reference: Scoredist: A simple and robust protein sequence distance estimator.
.IP
Erik LL Sonnhammer and Volker Hollich.
BMC Bioinformatics 6:108 (2005)
.IP
See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
.IP
Copyright (c) 2011\-2015: Genome Research Ltd.
Belvu is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
.TP
Version 4.44.1
14:27:56 Oct 19 2017
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.