Algorithm 2: The proposed BPINF algorithm for implementing FLAT
1: Input SeqA and SeqB; initialize the parameters: $t$, $T$, Inf_Rate, Spreed_Rate, Recovery_Rate
2: Initialize the population ($\mathrm{X}$) with ($N$) search agents, each ($x_i$), $i∊(1,N)$, locates two positions one in SeqA and the other in SeqB such that $x_i∊$ (Length (SeqA or SeqB) - LF)
3: Cut two fragments starting from the positions of ($x_i$) in the two sequences (SeqA and
SeqB)
4: Apply SW algorithm on each pair of fragments of each search agent ($x_i$), $i∊(1,N)$.
5: Compute the alignment score (length of near-exact LCCS found) for each search agent based on Eq. (1).
6: While (t$\le$T)
7: Update the first ($\alpha$) and second ($\beta$) best solutions from the population ($X$) based on the alignment score.
8: If (t$\le$$\frac{1}{2}$T)
9: Update each solution ($x_i$) based on BA's operator using Eqs. (2) - (6).
10: Else
11: Check the infection conditions for each solution ($x_i$):
12: IF ($(\alpha -D)<x_i<(\alpha +D)$)
13:  Infection ($i$) = 1
14: Else IF (rand () > Inf_Rate)
15:  Infection ($i$) = 1
16: Else
17:  Infection ($i$) = 0
18: End IF
19: For$\mathit{i}=1:\mathit{N}$
20: IF Infection ($i$) = 1
21:  Update the solution ($x_i$) toward ($\alpha$) based on Eqs. (11) - (12).
22: For$\mathit{p}=1:3$(propagate the infection through three agents)
23:  Select randomly one solution ($x_j$) , $j∊(1:N)$
24:  IF (rand () > Spread_Rate):
25:   Update the solution ($x_j$) toward ($x_i$) according to Eqs. (13) - (14).
26:   Infection ($j$) = 1
27:  End IF
28:  IF (rand () > Recovery_Rate): Infection ($j$) = 0 End IF
30: End For
31: IF (rand () > Recovery_Rate): Infection ($i$) = 0 End IF
32: Else
33: Update the solution ($x_i$) toward ($\beta$) based on Eq. (15) - (16)
34: End IF
35: End For
36: End IF
37: Cut two fragments starting from the positions of ($x_i$) in the two sequences (SeqA and SeqB)
Compute the alignment score for the search agents based on Eq. (1).
38: $\mathit{t}=\mathit{t}+1$;
39: End While
40: Output the near-exact LCCS pointed by the first best solution ($\alpha$) and its length.