While tools can generally find the optimal pairwise sequence alignment the same is not true for multiple alignments. The process used by the MathWorks multialign function will often provide a suboptimal solution. This tool can refine a multiple alignment to provide a more optimal solution, although it is not guaranteed to find the best possible solution. This tool splits the provided alignment, removes gaps, and then re-aligns the two profiles; if the new alignment has a better score then it is kept. This tool can use either a stochastic, deterministic or mixed method of determining how to split the alignment for the optimal score. This submission also includes .mat file with a large alignment of HIV-1 Env sequences which can be refined using this tool.