MUSCLE: multiple sequence alignment with high accuracy and high throughput.

@article{Edgar2004MUSCLEMS,
  title={MUSCLE: multiple sequence alignment with high accuracy and high throughput.},
  author={Robert C. Edgar},
  journal={Nucleic acids research},
  year={2004},
  volume={32 5},
  pages={
          1792-7
        }
}
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark… CONTINUE READING
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