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Selected highlights of the Phylogenetic Alignment literature

Features of phylogenetic alignment

  • PhylogeneticAlignment, aka StatisticalAlignment
    • aka StringTransducers, Evolutionary HMMs, Phylo-HMMs, Tree HMMs, Evolutionary SCFGs
  • Explicit probabilistic representations for evolutionary models
  • Stochastic grammars, sampled sequence trajectories on phylogenetic trees
  • Combined Bayesian inference of phylogeny and alignment


Deriving phyloalignment algorithms from indel models

Beyond point substitution models

RNA models

Protein models

Other papers following from TKF91

Reading the indel-rate signal

Reconstruction of indel history

In light of the interest in ancestral genome reconstruction, several authors have approached the problem of indel modeling from this slightly different direction. Typically these approaches require the input alignment to be specified and this leads the authors to a slightly different formalism, although the methods can still be reformulated within the framework of string transducers.

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Parents: DART
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