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Table 1 Pseudo code of the Monte-Carlo algorithm with simulated annealing

From: MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method

Input: T initial temperature

σ 0 initial ordering

T low low temperature

t constant number

σ =σ 0

While T > T low

   Repeat t time

choose random σ ~ ∈ N ( σ )

If η ( σ ~ ) ≤ η ( σ )

σ = σ ~

Else

x = random(0, 1)

If x < e − η ( σ ~ ) + ( σ ) T

σ = σ ~

   T = T * 0.9

Return σ and η(σ)