MOLE-BLAST is a tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple sequence alignment (MSA) between the query sequences along with their top BLAST database hits, and generates a phylogenetic tree. Query sequences in the tree are denoted with highlighted node labels. If the input sequences come from different genes or loci, MOLE-BLAST can cluster them and compute an MSA and a phylogenetic tree for each locus separately.