SYNOPSIS

belvu [options] <multiple_alignment>|- [X options]

<multiple_alignment>|- = alignment file or pipe.

DESCRIPTION

Belvu presents multiple sequence alignments in a colourful biologically interpretable manner.

OPTIONS

-c Print Conservation table.

-l <file> Load color code file.

-L <file> Load Markup 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.

-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>.

-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> Start up with tree calculated by method:

n -> Neighbor-joining u -> UPGMA N -> Neighbor-joining, only show tree U -> UPGMA, only show tree c -> Don't color tree by organism o -> Don't display sequence coordinates in tree s -> Use Storm & Sonnhammer distance correction r -> Use uncorrected distances

-b <#>

Print out # bootstrapped 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.

-g

Draw grid line (for debugging).

-u

Start up with uncoloured alignment (faster).

-h

Show this help.

-v

Show version info.

Some X options: -acefont <font> Main font. -font <font> Menu font.

AUTHOR

Erik Sonnhammer <[email protected]>

VERSION

Version 2.16, compiled Aug 18 2009