NAME
belvu - View multiple alignments in good-looking colours
DESCRIPTION
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Belvu - View multiple alignments in good-looking colours.
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Usage: belvu [options] <multiple_alignment>|-
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<multiple_alignment>|- = alignment file or pipe.
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Options:
- -c
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Print Conservation table.
- -l <file>
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Load residue color code file.
- -L <file>
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Load markup and organism color code file.
- -m <file>
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Read file with matching sequence segments.
- -r
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Read alignment in 'raw' format (Name sequence).
- -R
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Do not parse coordinates when reading alignment.
-o <format> Write alignment or tree to stdout in this format and exit.
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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
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Penalize gaps in pairwise comparisons.
- -i
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Ignore gaps in conservation calculation.
- -P
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Remove partial sequences at startup.
- -C
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Don't write coordinates to saved file.
- -z <char>
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Separator char between name and coordinates in saved file.
- -a
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Show alignment annotations on screen (Stockholm format only).
- -p
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Output random model probabilites for HMMER. (Based on all residues.)
- -S <order>
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Sort sequences in this order.
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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>
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Read in file of scores.
-T <method> Tree options:
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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
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(only in combination with Tree routines)
- -b <n>
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Apply boostrap analysis with <n> bootstrap samples
- -B
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Print out bootstrap trees and exit (Negative value -> display bootstrap trees on screen)
- -O <label>
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Read organism info after this label (default OS)
- -t <title>
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Set window title.
- -u
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Start up with uncoloured alignment (faster).
- -h, --help
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Show more detailed usage information
- --compiled
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Show package compile date
- --version
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Show package version number
- --abbrev-title-on
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Abbreviate window title prefixes
- --abbrev-title-off
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Do not abbreviate window title prefixes
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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).
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Written by Gemma Barson <[email protected]> Based on original code by Erik Sonnhammer <[email protected]>
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Reference: Scoredist: A simple and robust protein sequence distance estimator.
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Erik LL Sonnhammer and Volker Hollich. BMC Bioinformatics 6:108 (2005)
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See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
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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
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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.