RefineAlignments

A tool which can refine a set of multiple alignments to reduce the global alignment score.

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.