Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets

@article{Higgins1992SequenceOA,
  title={Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets},
  author={Desmond G. Higgins},
  journal={Computer applications in the biosciences : CABIOS},
  year={1992},
  volume={8 1},
  pages={
          15-22
        }
}
Ordination is a powerful method for analysing complex data sets but has been largely ignored in sequence analysis. This paper shows how to use principal coordinates analysis to find low-dimensional representations of distance matrices derived from aligned sets of sequences. The method takes a matrix of Euclidean distances between all pairs of sequence and finds a coordinate space where the distances are exactly preserved. The main problem is to find a measure of distance between aligned… CONTINUE READING

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