RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences.

@article{Hudelot2003RNAbasedPM,
  title={RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences.},
  author={Cendrine Hudelot and Vivek Gowri-Shankar and Howsun Jow and Magnus Rattray and Paul G. Higgs},
  journal={Molecular phylogenetics and evolution},
  year={2003},
  volume={28 2},
  pages={241-52}
}
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA… CONTINUE READING
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