Phylogenetic methods are becoming part of the standard method-ologies used in the analyses of biological sequence data, but several of the classical tools of phylogenetic inference were not designed with high throughput applications in mind. During our surveys, we haven't found software for the fast inference of neighbor joining trees from sequence alignments which could use biologically realistic substitution models with protein alignments. Thus, we developed quicktree-sd based on an efficient implementation of the neighbor joining algorithm, by implementing an amino acid distance correction based on Scoredist distances.