belvu1

Overview

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