Simple chained guide trees give high-quality protein multiple sequence alignments.

@article{Boyce2014SimpleCG,
  title={Simple chained guide trees give high-quality protein multiple sequence alignments.},
  author={Kieran Boyce and Fabian Sievers and Desmond G. Higgins},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2014},
  volume={111 29},
  pages={10556-61}
}
Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These… CONTINUE READING
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