BiologicalSequenceAnalysis 책 8장. Phylogeny의 확률론적 접근.

Contents

  1. Introduction
  2. Probabilistic models of evolution
  3. Calculating the likelihood for ungapped alignments
    1. The case of two sequences
    2. The likelihood for an arbitrary number of sequences
    3. Reversibility and independence of root position
  4. Using the likelihood for inference
    1. Maximising the likelihood
    2. Sampling from the posterior distribution
    3. A proposal distribution for phylogenetic trees
    4. The bootstrap revisited
  5. Towards more realistic evolutionary models
    1. Allowing different rates at different sites
    2. Evolutionary models with gaps
    3. Evaluating different probabilistic models
  6. Comparison of probabilistic and non-probabilistic methods
    1. A probabilistic interpretation of parsimony
    2. Maximum likelihood and pairwise distance methods
    3. A probabilistic interpretation of Sankoff & Cedergren
    4. Interpreting Hein's algorithm probabilistically

Introduction

Probabilistic models of evolution

Calculating the likelihood for ungapped alignments

The case of two sequences

The likelihood for an arbitrary number of sequences

Reversibility and independence of root position

Using the likelihood for inference

Maximising the likelihood

Sampling from the posterior distribution

A proposal distribution for phylogenetic trees

The bootstrap revisited

Towards more realistic evolutionary models

Allowing different rates at different sites

Evolutionary models with gaps

Evaluating different probabilistic models

Comparison of probabilistic and non-probabilistic methods

A probabilistic interpretation of parsimony

Maximum likelihood and pairwise distance methods

A probabilistic interpretation of Sankoff & Cedergren

Interpreting Hein's algorithm probabilistically

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