Lab 4: Phylogenetics - ricket-sjtu/bioinformatics GitHub Wiki

Stationary distribution of the nucleotides

$$ \pi = (\pi_A, \pi_C, \pi_G, \pi_T)^T $$

Substitution models

$$ \rho = \left( \begin{array}{cccc} a & b & c & d\\ e & f & g & h\\ i & j & k & l\\ m & o & p & q \end{array}\right) $$

Setting likelihood and prior models

General time reversible (GTR)

    lset applyto=() nst=6                           # GTR 
    lset applyto=() nst=6 rates=propinv             # GTR + I
    lset applyto=() nst=6 rates=gamma               # GTR + gamma
    lset applyto=() nst=6 rates=invgamma            # GTR + I + gamma

SYM

    lset applyto=() nst=6                           # SYM
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=6 rates=propinv             # SYM + I
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=6 rates=gamma               # SYM + gamma
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=6 rates=invgamma            # SYM + I + gamma
    prset applyto=() statefreqpr=fixed(equal)

HKY

    lset applyto=() nst=2                           # HKY
    lset applyto=() nst=2 rates=propinv             # HKY + I
    lset applyto=() nst=2 rates=gamma               # HKY + gamma
    lset applyto=() nst=2 rates=invgamma            # HKY + I + gamma

K2P

    lset applyto=() nst=2                           # K2P
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=2 rates=propinv             # K2P + I
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=2 rates=gamma               # K2P + gamma
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=2 rates=invgamma            # K2P + I + gamma
    prset applyto=() statefreqpr=fixed(equal)

F81

    lset applyto=() nst=1                           # F81
    lset applyto=() nst=1 rates=propinv             # F81 + I
    lset applyto=() nst=1 rates=gamma               # F81 + gamma
    lset applyto=() nst=1 rates=invgamma            # F81 + I + gamma

Jukes Cantor (JC)

    lset applyto=() nst=1                           # JC
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=1 rates=propinv             # JC + I
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=1 rates=gamma               # JC + gamma
    prset applyto=() statefreqpr=fixed(equal)

    lset applyto=() nst=1 rates=incgamma            # JC + I + gamma
    prset applyto=() statefreqpr=fixed(equal)