Models for DNA substitution

Table of Contents

Models for DNA substitution

http://www.stat.rice.edu/~mathbio/Polanski/stat655/

Plan

Nucleotides

Substitution

PPT Slide

Hypothesis

Other assumptions

Transition matrix

Models – discrete time

Jukes – Cantor model

Stationary distribution

Spectral decomposition of Pn

Remark

Kimura models

PPT Slide

Stationary distribution

Generalizations of Kimura models

Stationary distribution

Spectral decomposition

PPT Slide

Stationary distribution

Felsenstein model

Stationary distribution

HKY model

Eigenvalues of P

Left (row) eigenvectors

Right (column) eigenvectors

General 12 parameter model

Stationary distribution

Reversibility

Continuous – time models

Matrix of transition probabilites

Jukes – Cantor model

Spectral decomposition of P(t)

Kimura model

Spectral decomposition of P(t)

Parameter estimation

Jukes – Cantor model

Probability that the nucleotides are different in two descendants

Estimating p

Kimura model

PPT Slide

Email: kimmel@rice.edu

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