In this example, we use the genetic algorithm (-g) and optimise for gain (1), F/B (2) and SWR (16), while aiming for an input resistance of 12.5 Ohms.

parrot /export/home/drkirkby/yagiuda-1.18/src % optimise -g 19 -Z12.5 example1 1000
Will optimise using a genetic algorithm
Optimising for maximum possible gain.
Optimising for maximum possible FB ratio.
Optimising for an input SWR as low as possible
G= 9.65dBi,FB= 12.30dB,SL= 0.00dB,SWR= 5.18,Z= 42.42-j 29.86,0.328
    1 G= 9.35dBi,FB= 10.38dB,SL= 0.00dB,SWR= 3.04,Z= 12.44+j 14.57,0.387
    5 G= 8.55dBi,FB=  9.36dB,SL= 0.00dB,SWR= 1.84,Z= 20.54-j  5.77,0.420
    7 G= 9.29dBi,FB= 12.34dB,SL= 0.00dB,SWR= 2.32,Z= 28.40+j  3.72,0.427
    8 G= 8.71dBi,FB= 11.49dB,SL= 0.00dB,SWR= 1.86,Z= 17.96-j  7.76,0.429
    8 G= 9.67dBi,FB= 11.86dB,SL= 0.00dB,SWR= 2.17,Z= 25.51+j  5.55,0.454
    8 G= 9.13dBi,FB= 12.17dB,SL= 0.00dB,SWR= 1.78,Z= 14.39-j  7.64,0.457
    8 G= 9.30dBi,FB= 11.86dB,SL= 0.00dB,SWR= 1.44,Z= 17.81-j  1.39,0.495
    9 G= 9.66dBi,FB= 10.69dB,SL= 0.00dB,SWR= 1.27,Z= 15.63+j  1.04,0.529
   10 G= 9.63dBi,FB=  9.95dB,SL= 0.00dB,SWR= 1.21,Z= 15.07+j  0.12,0.533
   11 G= 9.50dBi,FB= 11.42dB,SL= 0.00dB,SWR= 1.17,Z= 14.55+j  0.45,0.535
   11 G=10.17dBi,FB= 11.06dB,SL= 0.00dB,SWR= 1.18,Z= 11.53+j  1.72,0.564
   18 G=10.17dBi,FB= 11.08dB,SL= 0.00dB,SWR= 1.09,Z= 11.48+j  0.32,0.575
   29 G=10.10dBi,FB= 11.33dB,SL= 0.00dB,SWR= 1.05,Z= 11.90-j  0.04,0.578
   33 G=10.11dBi,FB= 11.45dB,SL= 0.00dB,SWR= 1.05,Z= 11.96+j  0.10,0.579
   33 G=10.12dBi,FB= 11.57dB,SL= 0.00dB,SWR= 1.04,Z= 12.02+j  0.23,0.580
   45 G=10.11dBi,FB= 11.58dB,SL= 0.00dB,SWR= 1.04,Z= 12.04+j  0.23,0.580
   47 G=10.07dBi,FB= 11.59dB,SL= 0.00dB,SWR= 1.02,Z= 12.34+j  0.17,0.582
   49 G=10.06dBi,FB= 11.58dB,SL= 0.00dB,SWR= 1.02,Z= 12.38+j  0.17,0.582
   54 G=10.09dBi,FB= 11.70dB,SL= 0.00dB,SWR= 1.02,Z= 12.29+j  0.07,0.583
   57 G=10.08dBi,FB= 11.70dB,SL= 0.00dB,SWR= 1.01,Z= 12.34+j  0.06,0.583
   59 G=10.08dBi,FB= 11.69dB,SL= 0.00dB,SWR= 1.01,Z= 12.36+j  0.06,0.583
   62 G=10.07dBi,FB= 11.69dB,SL= 0.00dB,SWR= 1.01,Z= 12.41+j  0.06,0.583
   99 G=10.28dBi,FB= 12.49dB,SL= 0.00dB,SWR= 1.05,Z= 11.89+j  0.15,0.589
  100 G=10.21dBi,FB= 12.75dB,SL= 0.00dB,SWR= 1.02,Z= 12.32-j  0.13,0.592
  100 G=10.39dBi,FB= 13.66dB,SL= 0.00dB,SWR= 1.06,Z= 11.81-j  0.13,0.597
  101 G=10.39dBi,FB= 13.72dB,SL= 0.00dB,SWR= 1.06,Z= 11.86-j  0.18,0.597
  101 G=10.73dBi,FB= 11.03dB,SL= 0.00dB,SWR= 1.06,Z= 11.92+j  0.48,0.605
  110 G=10.74dBi,FB= 11.09dB,SL= 0.00dB,SWR= 1.06,Z= 11.91+j  0.42,0.606
  113 G=10.74dBi,FB= 11.01dB,SL= 0.00dB,SWR= 1.04,Z= 12.41+j  0.43,0.610
  117 G=10.74dBi,FB= 10.87dB,SL= 0.00dB,SWR= 1.02,Z= 12.28+j  0.09,0.612
  135 G=11.63dBi,FB= 18.12dB,SL= 0.00dB,SWR= 1.59,Z=  8.73-j  3.12,0.625
  143 G=11.68dBi,FB= 19.26dB,SL= 0.00dB,SWR= 1.71,Z=  8.41-j  3.75,0.630
  144 G=11.70dBi,FB= 19.72dB,SL= 0.00dB,SWR= 1.67,Z=  8.48-j  3.51,0.640
  145 G=11.68dBi,FB= 16.78dB,SL= 0.00dB,SWR= 1.24,Z= 11.25+j  2.18,0.652
  149 G=11.53dBi,FB= 17.96dB,SL= 0.00dB,SWR= 1.25,Z= 11.15+j  2.24,0.654
  151 G=11.58dBi,FB= 18.48dB,SL= 0.00dB,SWR= 1.23,Z= 11.06+j  1.93,0.664
  152 G=11.76dBi,FB= 18.76dB,SL= 0.00dB,SWR= 1.22,Z= 10.44+j  1.01,0.676
  156 G=11.74dBi,FB= 19.23dB,SL= 0.00dB,SWR= 1.20,Z= 10.63+j  0.97,0.683
  167 G=11.74dBi,FB= 19.23dB,SL= 0.00dB,SWR= 1.18,Z= 10.61+j  0.27,0.686
  168 G=11.75dBi,FB= 19.82dB,SL= 0.00dB,SWR= 1.21,Z= 10.43+j  0.65,0.691
  168 G=11.12dBi,FB= 24.86dB,SL= 0.00dB,SWR= 1.26,Z= 15.73+j  0.64,0.794
  170 G=11.17dBi,FB= 34.19dB,SL= 0.00dB,SWR= 1.19,Z= 14.29-j  1.56,0.935
  174 G=11.18dBi,FB= 37.25dB,SL= 0.00dB,SWR= 1.20,Z= 14.06-j  1.81,0.935
  179 G=11.19dBi,FB= 32.58dB,SL= 0.00dB,SWR= 1.19,Z= 14.12-j  1.59,0.937
  186 G=11.17dBi,FB= 35.02dB,SL= 0.00dB,SWR= 1.17,Z= 14.22+j  1.12,0.938
  191 G=11.32dBi,FB= 26.96dB,SL= 0.00dB,SWR= 1.13,Z= 14.09-j  0.12,0.947
  195 G=11.33dBi,FB= 28.27dB,SL= 0.00dB,SWR= 1.11,Z= 13.87-j  0.38,0.952
  205 G=11.32dBi,FB= 29.37dB,SL= 0.00dB,SWR= 1.11,Z= 13.31-j  1.09,0.952
  207 G=11.39dBi,FB= 27.16dB,SL= 0.00dB,SWR= 1.11,Z= 13.51-j  0.92,0.956
  501 G=11.69dBi,FB= 29.56dB,SL= 0.00dB,SWR= 1.13,Z= 12.06+j  1.44,0.967
  506 G=11.75dBi,FB= 27.15dB,SL= 0.00dB,SWR= 1.14,Z= 11.51+j  1.16,0.970
  508 G=11.71dBi,FB= 28.73dB,SL= 0.00dB,SWR= 1.12,Z= 11.76+j  1.18,0.970
  520 G=11.61dBi,FB= 29.20dB,SL= 0.00dB,SWR= 1.07,Z= 11.89+j  0.62,0.971
  536 G=11.64dBi,FB= 31.64dB,SL= 0.00dB,SWR= 1.08,Z= 11.64+j  0.41,0.971
  548 G=11.63dBi,FB= 31.09dB,SL= 0.00dB,SWR= 1.08,Z= 11.70+j  0.46,0.971
  572 G=11.50dBi,FB= 31.55dB,SL= 0.00dB,SWR= 1.01,Z= 12.60-j  0.14,0.974
  579 G=11.56dBi,FB= 43.43dB,SL= 0.00dB,SWR= 1.01,Z= 12.44-j  0.03,0.978
  584 G=11.64dBi,FB= 29.79dB,SL= 0.00dB,SWR= 1.02,Z= 12.39+j  0.17,0.980
  613 G=11.64dBi,FB= 30.11dB,SL= 0.00dB,SWR= 1.02,Z= 12.32+j  0.12,0.981
The best design is in a file "example1.bes". You should check it thoroughly
and if its better than example1, copy example1.bes to example1
parrot /export/home/drkirkby/yagiuda-1.18/src %

The last column of output shows a number that increases all the time. This is the goodness of the antenna. The GA uses this value and considers the antenna better if this number is bigger. The goodness is calculated from the a weighted average of the parameters you optimise for - in this case gain, FB and VSWR. We can set our own weighting factor if we wish. See #4.