Multi-locus sequence analysis (MLSA) involves using multiple genes or loci, usually conserved housekeeping genes, to construct phylogeny and other sequence-based analyses. Since different genes may have different mutation rates, MLSA generally gives a better approximation of underlying evolution and a more realistic resolution of phylogenetic relations among taxa than only one gene.
This is also a better alternative to ribosomal 16s/ITS-based analysis, especially for many bacterial species (including Bradyrhizobium, which I worked with), because the 16s/ITS are often very similar in these genera and cannot be used to differentiate species.
