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belvu: View multiple alignments in good-looking colours.

belvu - View multiple alignments in good-looking colours.
belvu [options] <multiple_alignment>|- [X options] <multiple_alignment>|- = alignment file or pipe.


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


-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.


For documentation, see: //www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html


Erik Sonnhammer <Erik.Sonnhammer@cgb.ki.se>
Version 2.16, compiled Aug 18 2009 BELVU(1)

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