Belvu is a multiple sequence alignment viewer and phylogenetic tool with an extensive set of user-configurable modes to color residues.

* View multiple sequence alignments. * Residues can be coloured by conservation, with user-configurable cutoffs and colours. * Residues can be coloured by residue type (user-configurable). * Colour schemes can be imported or exported. * Swissprot (or PIR) entries can be fetched by double clicking. * The position in the alignment can be easily tracked. * Manual deletion of rows and columns. * Automatic editing of rows and columns based on customisable criteria: - removal of all-gap columns; - removal of all gaps; - removal of redundant sequences; - removal of a column by a user-specified percentage of gaps; - filtering of sequences by percent identity; - removal of sequences by a user-specified percentage of gaps; - removal of partial sequences (those starting or ending with gaps); and - removal of columns by conservation (with user-specified upper/lower cutoffs). * The alignment can be saved in Stockholm, Selex, MSF or FASTA format. * Distance matrices between sequences can be generated using a variety of distance metrics. * Distance matrices can be imported or exported. * Phylogenetic trees can be constructed based on various distance-based tree reconstruction algorithms. * Trees can be saved in New Hampshire format. * Belvu can perform bootstrap phylogenetic reconstruction.