Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent

  title={Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent},
  author={Tandy J. Warnow},
  booktitle={PLoS currents},
BackgroundMost statistical methods for phylogenetic estimation in use today treat a gap (generally representing an insertion or deletion, i.e., indel) within the input sequence alignment as missing data. However, the statistical properties of this treatment of indels have not been fully investigated.ResultsWe prove that maximum likelihood phylogeny estimation, treating indels as missing data, can be statistically inconsistent for a general (and rather simple) model of sequence evolution, even… CONTINUE READING
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The impact of multiple protein sequence alignment on phylogenetic estimation

  • Wang L-S, J Leebens-Mack, PK Wall, K Beckmann, CW dePamphilis, T Warnow
  • IEEE/ACM Trans Comput Biol Bioinform
  • 2011
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