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In all cases, the community algorithm can be easily parallelized up to the machine level.
Possible next steps
——————–
We currently plan to extend the model-based variant as described in Section \[section:model-based\] with the following possibly useful variants of the alignment model:
– Fast static thresholding [@Rekers2007]
– Fast exact model-based alignment [@Mueller2013]
– Greedy balanced partitioning
We plan to do this for the model-free variant, too, starting with the version described in Section \[section:model-free\].
Conclusion
==========
We presented in this paper a new variant of the dynamic programming algorithm for multiple-sequence alignment, which we call the *community* algorithm. It is a hybrid approach, motivated by the model-free variant of the alignment model, but guided by the following principles: (1) the calculation of three scores is better than two, (2) a sparse, flat score vector is better than a dense, non-sparse score vector and (3) using the
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