.\" This file was generated by help2man 1.36 and then .\" manually tweaked a bit. .TH BELVU "1" "August 2009" "belvu 2.19" "User Commands" .SH NAME belvu \- View multiple alignments in good\-looking colours. .SH SYNOPSIS belvu [options] |\- [X options] .IP |\- = alignment file or pipe. .SH DESCRIPTION Belvu presents multiple sequence alignments in a colourful biologically interpretable manner. .SH OPTIONS \fB\-c\fR Print Conservation table. .HP \fB\-l\fR Load color code file. .HP \fB\-L\fR Load Markup color code file. .HP \fB\-m\fR Read file with matching sequence segments. .HP \fB\-r\fR Read alignment in 'raw' format (Name sequence). .HP \fB\-R\fR Do not parse coordinates when reading alignment. .HP \fB\-o\fR Write alignment or tree to stdout in this format and exit. .IP Valid formats: MSF, Mul(Stockholm), Selex, .IP FastaAlign, Fasta, tree. .HP \fB\-n\fR Make non\-redundant to %identity at startup. .HP \fB\-Q\fR Remove columns more gappy than . .HP \fB\-q\fR Remove sequences more gappy than . .TP \fB\-P\fR Remove partial sequences at startup. .TP \fB\-C\fR Don't write coordinates to saved file. .TP \fB\-z\fR Separator char between name and coordinates in saved file. .TP \fB\-a\fR Show alignment annotations on screen (Stockholm format only). .TP \fB\-p\fR Output random model probabilites for HMMER. .IP (Based on all residues.) .TP \fB\-S\fR Sort sequences in this order. .IP 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 .TP \fB\-s\fR Read in file of scores. .HP \fB\-T\fR Start up with tree calculated by method: .IP 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 .TP \fB\-b\fR <#> Print out # bootstrapped trees and exit .IP (Negative value \-> display bootstrap trees on screen) .TP \fB\-O\fR