acedb-other-belvu

multiple sequence alignment editor

For the analysis of biological sequences, a general principle is to corresponding regions between related proteins, RNA or DNA. Written next to each other, corresponding positions above each other, one has prepared an alignment. Belvu is best known for its perfect implementation of the Stockholm format of multiple sequence alignments, since upstream is maintaining that. That is for instance used in the Pfam and Rfam databases.

belvu

multiple sequence alignment viewer and phylogenetic tool

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.