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



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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.

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MATLAB Release
MATLAB 7.9 (R2009b)

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