Provided by: belvu_4.44.1+dfsg-2build1_amd64
belvu - View multiple alignments in good-looking colours
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@example.com> Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se> 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
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.