lectures N.6, 7, 8 and 9

Life is physics (Goldenberg-Woese)

What is evolution (HA 3.1), the naïve setting: mutation-selection (HA 3.2)

Species/speciation

The space of biological sequences as the archive of evolution (Molecules as documents of Evolutionary History (see: ZuckerkandlPauling1965)

Mutations (HA 3.2), sequence variation within and between species (HA 3.3)

Negative purifying vs positive Darwinian selectionEevolutionary pressure on a site through dn/ds [Ka/Ks] (optional) (HA 11.2.3)

Evolutionary distances between orthologous genes (HA 4.1.1)

Probabilistic models of evolution (DU chap 8.2)

The Jukes-Cantor model (HA 4.1.2 and Box 4.1)

Generative probabilistic models of sequence evolution: general scheme (HA 4.1)

Alphabets, symbols, states

Transition rates matrix

Dynamics between states: Master equations: in /out terms

Detailed balance

Alignments (genes/proteins)

Orthology paralogy, homology

The genetic code: codon bias

Why probabilistic evolutionary models?

substitution matrices (DU 2.2, Protein Substitutions Models (slides))

PAM model of protein sequence evolution (HA 4.2)

PAM distances (HA box 4.2)

Log-odd scoring PAM matrices (HA 4.3.1, DU chap 2)

BLOSUM scoring matrices (HA 4.3.3, DU chap.2)

STUDY MATERIALS IN CB_23_24_PACK_5