Direct optimization, affine gap costs, and node stability.

  title={Direct optimization, affine gap costs, and node stability.},
  author={Lone Aagesen},
  journal={Molecular phylogenetics and evolution},
  volume={36 3},
  • Lone Aagesen
  • Published 2005 in Molecular phylogenetics and evolution
The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Robustness to changes in parameter costs is therefore a desired quality of a data set because the final conclusions will be less dependent on selecting a precise optimal cost set. Here, node stability is explored in relationship to separate versus combined analysis in three different data sets, all including several data partitions… CONTINUE READING

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