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Table 4 Proposal distributions.

From: Identifying dramatic selection shifts in phylogenetic trees

Param.

Proposal Distribution

Tuning Param.

MH Ratio

κ

κ* = κ exp [κ t (U - 0.5)], U ~ Unif(0, 1)

κ t = 1.0

α

α* ~ Normal(α, α t )

α t = 0.5

t i

= t i exp [t t (U - 0.5)], U ~ Unif(0, 1)

t t = 1.0

θ

θ* ~ Normal(θ, θ t )

θ t = 0.2

l* ~ Normal(l, l t )

l t = 0.2

 

b* ~ Unif(1,...,2N - 3), l* ~ Unif(0, 1)

NA

d

d* = 1 - d

NA

  1. For each parameter listed, a new value (starred, e.g. κ*) is proposed according to the listed distribution. Branch lengths t i are updated one at a time for i = 1,...,2N - 3. Tuning parameters are subscripted by t. Updates of either l or (b, l) are mixed with probability m t . Update of d is a trans-dimensional move. The Metropolis-Hastings acceptance ratios are given in the last column. Dependence on parameters not involved in the update is not shown.