Skip to main content

Table 6 Average Robinson–Foulds (RF) errors for IDQPSO, Simulated Annealing and GRAPPA

From: Achieving large and distant ancestral genome inference by using an improved discrete quantum-behaved particle swarm optimization algorithm

Program RF error (%) (No transposition)
r = 20 r = 40 r = 60 r = 80 r = 100 r = 120 r = 140 r = 160 r = 180
IDQPSO-Median 0 0 0 0 0 0 2.5 2.5 3.8
SA-Median 0 0 0 2.5 0 2.5 6.3 5.0 10.0
GRAPPA-Exact 0 0 0 0
Neighbor-joining 0 0 0 2.5 6.3 6.3 12.5 20 20
Program RF error (%) (90% Inversion/10% transposition)
r = 20 r = 40 r = 60 r = 80 r = 100 r = 120 r = 140 r = 160 r = 180
IDQPSO-Median 0 0 0 0 0 2.5 2.5 2.5 8.8
SA-Median 0 0 0 0 0 2.5 3.8 3.8 12.5
GRAPPA-Exact 0 0 0
Neighbor-joining 0 0 0 0 3.8 13.8 16.3 23.8 30
  1. – indicates a program cannot finish after 5 days of computation. For the IDQPSO and Simulated Annealing methods, results for \(r\ge 140\) are from the best trees obtained within 5 days of computation
  2. The best values of all the compared algorithms are indicated in italics