Read instructions on how to install Belvu.
In addition, Belvu is a phylogenetic tool. It can be used to generate distance matrices between sequences under a selection of distance metrics. These can be saved and used subsequently in other applications. Belvu also implements certain distance-based tree reconstruction algorithms - including import of externally generated distance matrices - and bootstrap phylogenetic reconstruction. These functions are available both in the GUI (meaning Belvu may also be used as a tree viewer) or as command-line options, making the program a potential component in phylogenetic software pipelines.
Belvu - View multiple alignments in pretty colours.
Usage: belvu [options] < multiple_alignment > | - [X options]
< multiple_alignment > | - = file or pipe in Pfam/selex/MSF format (see below).
Options:
-r Alignment is in 'raw' format.
Example of raw alignment file:
seq1_name MFILKTP
seq1_name MYI.RTP
-l < file > Load color code file.
Format: < symbol > < color >
(Lines starting with # are ignored (comment lines))
Example of color code file:
# Aroma
F YELLOW
Y YELLOW
W YELLOW
# Yuck
D RED
N GREEN
X BLUE
Available colors:
WHITE
BLACK
LIGHTGRAY
DARKGRAY
RED
GREEN
BLUE
YELLOW
CYAN
MAGENTA
LIGHTRED
LIGHTGREEN
LIGHTBLUE
DARKRED
DARKGREEN
DARKBLUE
PALERED
PALEGREEN
PALEBLUE
PALEYELLOW
PALECYAN
PALEMAGENTA
BROWN
ORANGE
PALEORANGE
PURPLE
VIOLET
PALEVIOLET
GRAY
PALEGRAY
CERISE
MIDBLUE
-L < file> Load markup and organism color code file.
Colour the markup text by residue or colour organism in tree.
Example to set color of letters A and B:
A GREEN
B YELLOW
Example to set color of organism human:
#=OS BLUE human
-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 <#> Print UPGMA-based subfamilies at cutoff #.
-n < cutoff> Make non-redundant to %identity at startup.
-Q < cutoff> Remove columns more gappy than .
-q < cutoff> Remove sequences more gappy than .
-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
-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 <#> Apply boostrap analysis with # 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)
-u Start up with uncoloured alignment (faster).
-c Print Conservation table.
-s < file > Read in file of scores. A column with scores will
automatically appear after the coordinates.
Format: < score > < sequence_id >
Example of score file:
2.78 seq_1/180-206
2.78 seq_2/180-206
3.79 seq_3/42-94
-t < title > Set window title.
-g Draw grid line (for debugging).
-m < file > Read file with matching sequences segments. This is used to
display a match of a query sequence to a family. The format
of the match is :
Line 1: Name/start-end score
Line 2: Query sequence in matching segment, no pads!
Line 3: Sequence of matching segments (qstart1 qend1 fstart1
fend2 qstart2 qend2 fstart2 fend2 etc...).
Example:
ZK673.9/238-260 21.58
CPENWVQFTGNGTQYGVCLRGFT
1 2 1 2 4 7 8 11
NOTE: A sometimes easier way of doing this is to concatenate
the match to the end of the alignment, after a line with
exactly this string within the quotes: "# matchFooter"
Some X options:
-acefont < font> Main font.
-font < font> Menu font.
Note: X options only work after "setenv POSIXLY_CORRECT"
setenv BELVU_FETCH to desired sequence fetching program.
In other words, to get going, just type 'belvu my_alignment' and it
should work. It detects if it is in MSF, selex or Pfam format (see
below), but you have to tell it if it is in 'raw' format (Name
sequence).NOTE: Make sure that all sequence names are unique - very funny thing happen if they are not.
For compatibility with the old SELEX format, #=RF is also accepted by Belvu as if it were "#=GC #=RF".
To go from a sequence alignment to a tree shown on screen, consider the following options.
-oWrite alignment or tree to stdout in this format and exit. Valid formats: MSF, Mul(Stockholm), Selex, FastaAlign, Fasta, tree. ... -T 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 <#> Apply boostrap analysis with # bootstrap samples -B Print out bootstrap trees and exit (Negative value -> display bootstrap trees on screen)
A B C 0 10 20 15 0 15 25 5 0