Integrated gene and species phylogenies from unaligned whole genome protein sequences

@article{Stuart2002IntegratedGA,
  title={Integrated gene and species phylogenies from unaligned whole genome protein sequences},
  author={Gary W. Stuart and Karen Moffett and Steve Baker},
  journal={Bioinformatics},
  year={2002},
  volume={18 1},
  pages={100-8}
}
MOTIVATION Most molecular phylogenies are based on sequence alignments. Consequently, they fail to account for modes of sequence evolution that involve frequent insertions or deletions. Here we present a method for generating accurate gene and species phylogenies from whole genome sequence that makes use of short character string matches not placed within explicit alignments. In this work, the singular value decomposition of a sparse tetrapeptide frequency matrix is used to represent the… CONTINUE READING

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