Running GARLI Version 1.0.695 (10 Dec 2009) ->MPI Parallel Version<- Note: this version divides a number of independent runs across processors. It is not the multipopulation parallel Garli algorithm. (but is generally a better use of resources) Compiled May 5 2010 08:06:04 using Intel icc compiler version 10.10 Using NCL version 2.1.10 ####################################################### Reading config file garli.conf Attempting to read data file in Nexus format (using NCL): infile ... Reading TAXA block... successful Reading CHARACTERS block... found dna data... successful Reading TREES block... successful ####################################################### Summary of dataset: 12 sequences. 259 constant characters. 119 parsimony-informative characters. 54 uninformative variable characters. 432 total characters. 155 unique patterns in compressed data matrix. ####################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 2560.0 MB of memory. Garli will actually use approx. 2.9 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### >>>Bootstrap rep 1 (of 1) Search rep 1 (of 2)<<< Random seed for bootstrap reweighting: 108415 MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2035 0.2515 0.3056 0.2394 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1499 Substitution rate categories under this model: rate proportion 0.0000 0.1499 0.0334 0.2125 0.2519 0.2125 0.8203 0.2125 2.8944 0.2125 Starting with seed=714658527 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 Optimizing parameters... improved 0.002 lnL Optimizing branchlengths... improved 0.000 lnL 8 9 10 11 12 Initial ln Likelihood: -2092.1256 optimizing starting branch lengths and model parameters... pass 1 : + 12.9198 (branch= 1.45 scale= 0.70 alpha= 0.00 pinv= 0.00 equil freqs= 5.15 rel rates= 5.61) pass 2 : + 2.5580 (branch= 1.09 scale= 0.00 alpha= 0.00 pinv= 0.00 equil freqs= 1.47 rel rates= 0.00) pass 3 : + 0.0311 (branch= 0.00 scale= 0.00 alpha= 0.00 pinv= 0.00 equil freqs= 0.03 rel rates= 0.00) lnL after optimization: -2076.6168 gen current_lnL precision last_tree_imp 0 -2076.6168 0.500 0 100 -2071.1307 0.500 59 200 -2068.7418 0.500 120 300 -2068.5525 0.500 120 400 -2067.8924 0.500 120 500 -2067.7482 0.500 120 600 -2067.6470 0.500 120 700 -2067.3990 0.500 120 opt. precision reduced, optimizing branchlengths:-2067.3990 -> -2067.3926 800 -2067.2461 0.475 120 900 -2067.1604 0.475 120 1000 -2067.0398 0.475 120 1100 -2066.9666 0.475 120 1200 -2066.8469 0.475 120 opt. precision reduced, optimizing branchlengths:-2066.8469 -> -2066.8469 1300 -2066.6100 0.451 120 1400 -2066.4932 0.451 120 1500 -2066.4396 0.451 120 1600 -2066.4266 0.451 120 1700 -2066.4143 0.451 120 opt. precision reduced, optimizing branchlengths:-2066.4143 -> -2066.4143 1800 -2066.4074 0.426 120 1900 -2066.3961 0.426 120 2000 -2066.3846 0.426 120 2100 -2066.3764 0.426 120 2200 -2066.3730 0.426 120 opt. precision reduced, optimizing branchlengths:-2066.3730 -> -2066.3730 2300 -2066.3723 0.402 120 2400 -2066.3560 0.402 120 2500 -2066.3557 0.402 120 2600 -2066.3552 0.402 120 2700 -2066.3516 0.402 120 opt. precision reduced, optimizing branchlengths:-2066.3516 -> -2066.3516 2800 -2066.3501 0.377 120 2900 -2066.3485 0.377 120 3000 -2066.3485 0.377 120 3100 -2066.3462 0.377 120 3200 -2066.3436 0.377 120 opt. precision reduced, optimizing branchlengths:-2066.3436 -> -2066.3436 3300 -2066.3428 0.353 120 3400 -2066.3428 0.353 120 3500 -2066.3428 0.353 120 3600 -2066.3410 0.353 120 3700 -2066.3395 0.353 120 opt. precision reduced, optimizing branchlengths:-2066.3395 -> -2066.3395 3800 -2066.3395 0.328 120 3900 -2066.3392 0.328 120 4000 -2066.3392 0.328 120 4100 -2066.3390 0.328 120 4200 -2066.3390 0.328 120 opt. precision reduced, optimizing branchlengths:-2066.3390 -> -2066.3390 4300 -2066.3390 0.304 120 4400 -2066.3387 0.304 120 4500 -2066.3352 0.304 120 4600 -2066.3348 0.304 120 4700 -2066.3348 0.304 120 opt. precision reduced, optimizing branchlengths:-2066.3348 -> -2066.3348 4800 -2066.3336 0.279 120 4900 -2066.3336 0.279 120 5000 -2066.3334 0.279 120 5100 -2066.3334 0.279 120 5200 -2066.3334 0.279 120 opt. precision reduced, optimizing branchlengths:-2066.3334 -> -2066.3334 5300 -2066.3327 0.255 120 5400 -2066.3327 0.255 120 5500 -2066.3327 0.255 120 5600 -2066.3327 0.255 120 5700 -2066.3327 0.255 120 opt. precision reduced, optimizing branchlengths:-2066.3327 -> -2066.3327 5800 -2066.3327 0.230 120 5900 -2066.3320 0.230 120 6000 -2066.3320 0.230 120 6100 -2066.3319 0.230 120 6200 -2066.3315 0.230 120 opt. precision reduced, optimizing branchlengths:-2066.3315 -> -2066.3315 6300 -2066.3315 0.206 120 6400 -2066.3315 0.206 120 6500 -2066.3315 0.206 120 6600 -2066.3313 0.206 120 6700 -2066.3313 0.206 120 opt. precision reduced, optimizing branchlengths:-2066.3313 -> -2066.3313 6800 -2066.3313 0.181 120 6900 -2066.3313 0.181 120 7000 -2066.3307 0.181 120 7100 -2066.3307 0.181 120 7200 -2066.3307 0.181 120 opt. precision reduced, optimizing branchlengths:-2066.3307 -> -2066.3307 7300 -2066.3307 0.157 120 7400 -2066.3302 0.157 120 7500 -2066.3302 0.157 120 7600 -2066.3302 0.157 120 7700 -2066.3302 0.157 120 opt. precision reduced, optimizing branchlengths:-2066.3302 -> -2066.3302 7800 -2066.3302 0.132 120 7900 -2066.3302 0.132 120 8000 -2066.3302 0.132 120 8100 -2066.3302 0.132 120 8200 -2066.3302 0.132 120 opt. precision reduced, optimizing branchlengths:-2066.3302 -> -2066.3302 8300 -2066.3302 0.108 120 8400 -2066.3291 0.108 120 8500 -2066.3289 0.108 120 8600 -2066.3289 0.108 120 8700 -2066.3289 0.108 120 opt. precision reduced, optimizing branchlengths:-2066.3289 -> -2066.3289 8800 -2066.3285 0.083 120 8900 -2066.3285 0.083 120 9000 -2066.3285 0.083 120 9100 -2066.3285 0.083 120 9200 -2066.3285 0.083 120 opt. precision reduced, optimizing branchlengths:-2066.3285 -> -2066.3285 9300 -2066.3285 0.059 120 9400 -2066.3285 0.059 120 9500 -2066.3285 0.059 120 9600 -2066.3284 0.059 120 9700 -2066.3270 0.059 120 opt. precision reduced, optimizing branchlengths:-2066.3270 -> -2066.3270 9800 -2066.3270 0.034 120 9900 -2066.3270 0.034 120 10000 -2066.3270 0.034 120 10100 -2066.3270 0.034 120 10200 -2066.3270 0.034 120 opt. precision reduced, optimizing branchlengths:-2066.3270 -> -2066.3082 10300 -2066.3081 0.010 120 10400 -2066.3081 0.010 120 10500 -2066.3081 0.010 120 10600 -2066.3081 0.010 120 10700 -2066.3081 0.010 120 10800 -2066.3081 0.010 120 10900 -2066.3081 0.010 120 11000 -2066.3081 0.010 120 11100 -2066.3081 0.010 120 11200 -2066.3081 0.010 120 11300 -2066.3081 0.010 120 11400 -2066.3081 0.010 120 11500 -2066.3080 0.010 120 11600 -2066.3080 0.010 120 11700 -2066.3080 0.010 120 11800 -2066.3080 0.010 120 11900 -2066.3080 0.010 120 12000 -2066.3080 0.010 120 12100 -2066.3079 0.010 120 12200 -2066.3079 0.010 120 12300 -2066.3079 0.010 120 12400 -2066.3079 0.010 120 12500 -2066.3079 0.010 120 12600 -2066.3079 0.010 120 12700 -2066.3079 0.010 120 12800 -2066.3079 0.010 120 12900 -2066.3079 0.010 120 13000 -2066.3079 0.010 120 13100 -2066.3079 0.010 120 13200 -2066.3079 0.010 120 13300 -2066.3079 0.010 120 13400 -2066.3079 0.010 120 13500 -2066.3079 0.010 120 13600 -2066.3079 0.010 120 13700 -2066.3079 0.010 120 13800 -2066.3079 0.010 120 13900 -2066.3079 0.010 120 14000 -2066.3077 0.010 120 14100 -2066.3077 0.010 120 14200 -2066.3077 0.010 120 14300 -2066.3077 0.010 120 14400 -2066.3077 0.010 120 14500 -2066.3077 0.010 120 14600 -2066.3077 0.010 120 14700 -2066.3077 0.010 120 14800 -2066.3077 0.010 120 14900 -2066.3077 0.010 120 15000 -2066.3077 0.010 120 15100 -2066.3077 0.010 120 15200 -2066.3077 0.010 120 15300 -2066.3077 0.010 120 15400 -2066.3077 0.010 120 15500 -2066.3077 0.010 120 15600 -2066.3075 0.010 120 15700 -2066.3075 0.010 120 15800 -2066.3075 0.010 120 15900 -2066.3075 0.010 120 16000 -2066.3075 0.010 120 16100 -2066.3075 0.010 120 16200 -2066.3075 0.010 120 16300 -2066.3075 0.010 120 16400 -2066.3075 0.010 120 16500 -2066.3075 0.010 120 16600 -2066.3075 0.010 120 16700 -2066.3075 0.010 120 16800 -2066.3075 0.010 120 16900 -2066.3075 0.010 120 17000 -2066.3075 0.010 120 17100 -2066.3075 0.010 120 17200 -2066.3075 0.010 120 17300 -2066.3075 0.010 120 17400 -2066.3075 0.010 120 17500 -2066.3075 0.010 120 17600 -2066.3075 0.010 120 17700 -2066.3075 0.010 120 17800 -2066.3074 0.010 120 17900 -2066.3074 0.010 120 18000 -2066.3074 0.010 120 18100 -2066.3074 0.010 120 18200 -2066.3074 0.010 120 18300 -2066.3074 0.010 120 18400 -2066.3074 0.010 120 18500 -2066.3074 0.010 120 18600 -2066.3074 0.010 120 18700 -2066.3074 0.010 120 18800 -2066.3074 0.010 120 18900 -2066.3074 0.010 120 19000 -2066.3074 0.010 120 19100 -2066.3074 0.010 120 19200 -2066.3074 0.010 120 19300 -2066.3074 0.010 120 19400 -2066.3074 0.010 120 19500 -2066.3074 0.010 120 19600 -2066.3074 0.010 120 19700 -2066.3074 0.010 120 19800 -2066.3074 0.010 120 19900 -2066.3074 0.010 120 20000 -2066.3074 0.010 120 20100 -2066.3074 0.010 120 20200 -2066.3074 0.010 120 20300 -2066.3074 0.010 120 20400 -2066.3074 0.010 120 20500 -2066.3074 0.010 120 20600 -2066.3074 0.010 120 20700 -2066.3074 0.010 120 20800 -2066.3074 0.010 120 20900 -2066.3074 0.010 120 21000 -2066.3074 0.010 120 21100 -2066.3074 0.010 120 21200 -2066.3074 0.010 120 21300 -2066.3074 0.010 120 21400 -2066.3074 0.010 120 21500 -2066.3074 0.010 120 21600 -2066.3074 0.010 120 21700 -2066.3074 0.010 120 21800 -2066.3074 0.010 120 21900 -2066.3074 0.010 120 22000 -2066.3074 0.010 120 22100 -2066.3074 0.010 120 22200 -2066.3074 0.010 120 22300 -2066.3074 0.010 120 22400 -2066.3074 0.010 120 22500 -2066.3074 0.010 120 22600 -2066.3074 0.010 120 22700 -2066.3074 0.010 120 22800 -2066.3073 0.010 120 22900 -2066.3073 0.010 120 23000 -2066.3073 0.010 120 23100 -2066.3073 0.010 120 23200 -2066.3073 0.010 120 23300 -2066.3073 0.010 120 23400 -2066.3073 0.010 120 23500 -2066.3073 0.010 120 23600 -2066.3073 0.010 120 23700 -2066.3073 0.010 120 23800 -2066.3073 0.010 120 23900 -2066.3073 0.010 120 24000 -2066.3073 0.010 120 24100 -2066.3073 0.010 120 24200 -2066.3073 0.010 120 24300 -2066.3073 0.010 120 24400 -2066.3073 0.010 120 24500 -2066.3073 0.010 120 24600 -2066.3073 0.010 120 24700 -2066.3073 0.010 120 24800 -2066.3073 0.010 120 24900 -2066.3073 0.010 120 25000 -2066.3073 0.010 120 25100 -2066.3073 0.010 120 25200 -2066.3073 0.010 120 25300 -2066.3073 0.010 120 25400 -2066.3073 0.010 120 25500 -2066.3073 0.010 120 25600 -2066.3073 0.010 120 25700 -2066.3073 0.010 120 25800 -2066.3073 0.010 120 25900 -2066.3073 0.010 120 26000 -2066.3073 0.010 120 26100 -2066.3073 0.010 120 26200 -2066.3073 0.010 120 26300 -2066.3073 0.010 120 26400 -2066.3073 0.010 120 26500 -2066.3073 0.010 120 26600 -2066.3073 0.010 120 26700 -2066.3073 0.010 120 26800 -2066.3073 0.010 120 26900 -2066.3073 0.010 120 27000 -2066.3073 0.010 120 27100 -2066.3072 0.010 120 27200 -2066.3072 0.010 120 27300 -2066.3072 0.010 120 27400 -2066.3072 0.010 120 27500 -2066.3072 0.010 120 27600 -2066.3072 0.010 120 27700 -2066.3072 0.010 120 27800 -2066.3072 0.010 120 27900 -2066.3072 0.010 120 28000 -2066.3072 0.010 120 28100 -2066.3072 0.010 120 28200 -2066.3072 0.010 120 28300 -2066.3072 0.010 120 28400 -2066.3072 0.010 120 28500 -2066.3072 0.010 120 28600 -2066.3072 0.010 120 28700 -2066.3072 0.010 120 28800 -2066.3072 0.010 120 28900 -2066.3072 0.010 120 29000 -2066.3072 0.010 120 29100 -2066.3072 0.010 120 29200 -2066.3072 0.010 120 29300 -2066.3072 0.010 120 29400 -2066.3072 0.010 120 29500 -2066.3072 0.010 120 29600 -2066.3072 0.010 120 29700 -2066.3072 0.010 120 29800 -2066.3072 0.010 120 29900 -2066.3072 0.010 120 30000 -2066.3072 0.010 120 30100 -2066.3072 0.010 120 30200 -2066.3072 0.010 120 30300 -2066.3072 0.010 120 Reached termination condition! last topological improvement at gen 120 Improvement over last 500 gen = 0.00000 Current score = -2066.3072 Performing final optimizations... pass 1 : -2066.3072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 2 : -2066.3072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 3 : -2066.3072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 4 : -2066.3072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 5 : -2066.3072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 6 : -2066.3070 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 7 : -2066.3069 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 8 : -2066.3069 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 9 : -2066.3068 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 10: -2066.3068 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 11: -2066.3067 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 12: -2066.3067 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -2066.3067 Time used so far = 0 hours, 2 minutes and 45 seconds MODEL REPORT - Parameter values are FINAL Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.483, AG = 2.797, AT = 1.497, CG = 0.868, CT = 4.605, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2006 0.2389 0.2833 0.2772 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5297 with an invariant (invariable) site category, proportion estimated 0.1464 Substitution rate categories under this model: rate proportion 0.0000 0.1464 0.0390 0.2134 0.2709 0.2134 0.8407 0.2134 2.8494 0.2134 >>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 2)<<< >>>Bootstrap rep 1 (of 1) Search rep 2 (of 2)<<< Starting with seed=725073307 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 Optimizing parameters... improved 0.002 lnL Optimizing branchlengths... improved 7.020 lnL 8 9 10 11 12 Initial ln Likelihood: -2099.7661 optimizing starting branch lengths and model parameters... pass 1 : + 13.6157 (branch= 2.77 scale= 0.00 alpha= 0.00 pinv= 0.00 equil freqs= 5.63 rel rates= 5.22) pass 2 : + 2.3019 (branch= 0.89 scale= 0.00 alpha= 0.00 pinv= 0.00 equil freqs= 1.41 rel rates= 0.00) pass 3 : + 0.4021 (branch= 0.37 scale= 0.00 alpha= 0.00 pinv= 0.00 equil freqs= 0.03 rel rates= 0.00) lnL after optimization: -2083.4464 gen current_lnL precision last_tree_imp 0 -2083.4464 0.500 0 100 -2070.3786 0.500 70 200 -2068.7202 0.500 125 300 -2068.2292 0.500 125 400 -2067.8837 0.500 125 500 -2067.5600 0.500 125 600 -2067.4816 0.500 125 700 -2067.2809 0.500 125 opt. precision reduced, optimizing branchlengths:-2067.2809 -> -2067.2764 800 -2067.0138 0.475 125 900 -2066.9176 0.475 125 1000 -2066.8525 0.475 125 1100 -2066.7629 0.475 125 1200 -2066.6789 0.475 125 opt. precision reduced, optimizing branchlengths:-2066.6789 -> -2066.6774 1300 -2066.5644 0.451 125 1400 -2066.5040 0.451 125 1500 -2066.4512 0.451 125 1600 -2066.4229 0.451 125 1700 -2066.4218 0.451 125 opt. precision reduced, optimizing branchlengths:-2066.4218 -> -2066.4218 1800 -2066.4055 0.426 125 1900 -2066.3991 0.426 125 2000 -2066.3835 0.426 125 2100 -2066.3811 0.426 125 2200 -2066.3788 0.426 125 opt. precision reduced, optimizing branchlengths:-2066.3788 -> -2066.3788 2300 -2066.3737 0.402 125 2400 -2066.3736 0.402 125 2500 -2066.3680 0.402 125 2600 -2066.3588 0.402 125 2700 -2066.3519 0.402 125 opt. precision reduced, optimizing branchlengths:-2066.3519 -> -2066.3519 2800 -2066.3503 0.377 125 2900 -2066.3483 0.377 125 3000 -2066.3473 0.377 125 3100 -2066.3465 0.377 125 3200 -2066.3449 0.377 125 opt. precision reduced, optimizing branchlengths:-2066.3449 -> -2066.3449 3300 -2066.3446 0.353 125 3400 -2066.3444 0.353 125 3500 -2066.3441 0.353 125 3600 -2066.3440 0.353 125 3700 -2066.3440 0.353 125 opt. precision reduced, optimizing branchlengths:-2066.3440 -> -2066.3440 3800 -2066.3435 0.328 125 3900 -2066.3435 0.328 125 4000 -2066.3424 0.328 125 4100 -2066.3424 0.328 125 4200 -2066.3423 0.328 125 opt. precision reduced, optimizing branchlengths:-2066.3423 -> -2066.3423 4300 -2066.3423 0.304 125 4400 -2066.3422 0.304 125 4500 -2066.3422 0.304 125 4600 -2066.3416 0.304 125 4700 -2066.3416 0.304 125 opt. precision reduced, optimizing branchlengths:-2066.3416 -> -2066.3416 4800 -2066.3415 0.279 125 4900 -2066.3412 0.279 125 5000 -2066.3412 0.279 125 5100 -2066.3409 0.279 125 5200 -2066.3409 0.279 125 opt. precision reduced, optimizing branchlengths:-2066.3409 -> -2066.3409 5300 -2066.3403 0.255 125 5400 -2066.3403 0.255 125 5500 -2066.3402 0.255 125 5600 -2066.3399 0.255 125 5700 -2066.3399 0.255 125 opt. precision reduced, optimizing branchlengths:-2066.3399 -> -2066.3399 5800 -2066.3395 0.230 125 5900 -2066.3391 0.230 125 6000 -2066.3391 0.230 125 6100 -2066.3391 0.230 125 6200 -2066.3391 0.230 125 opt. precision reduced, optimizing branchlengths:-2066.3391 -> -2066.3391 6300 -2066.3391 0.206 125 6400 -2066.3391 0.206 125 6500 -2066.3391 0.206 125 6600 -2066.3391 0.206 125 6700 -2066.3391 0.206 125 opt. precision reduced, optimizing branchlengths:-2066.3391 -> -2066.3391 6800 -2066.3391 0.181 125 6900 -2066.3391 0.181 125 7000 -2066.3391 0.181 125 7100 -2066.3391 0.181 125 7200 -2066.3391 0.181 125 opt. precision reduced, optimizing branchlengths:-2066.3391 -> -2066.3391 7300 -2066.3391 0.157 125 7400 -2066.3384 0.157 125 7500 -2066.3381 0.157 125 7600 -2066.3381 0.157 125 7700 -2066.3381 0.157 125 opt. precision reduced, optimizing branchlengths:-2066.3381 -> -2066.3381 7800 -2066.3358 0.132 125 7900 -2066.3358 0.132 125 8000 -2066.3345 0.132 125 8100 -2066.3345 0.132 125 8200 -2066.3338 0.132 125 opt. precision reduced, optimizing branchlengths:-2066.3338 -> -2066.3338 8300 -2066.3336 0.108 125 8400 -2066.3336 0.108 125 8500 -2066.3335 0.108 125 8600 -2066.3335 0.108 125 8700 -2066.3335 0.108 125 opt. precision reduced, optimizing branchlengths:-2066.3335 -> -2066.3335 8800 -2066.3322 0.083 125 8900 -2066.3322 0.083 125 9000 -2066.3322 0.083 125 9100 -2066.3322 0.083 125 9200 -2066.3317 0.083 125 opt. precision reduced, optimizing branchlengths:-2066.3317 -> -2066.3317 9300 -2066.3298 0.059 125 9400 -2066.3298 0.059 125 9500 -2066.3296 0.059 125 9600 -2066.3296 0.059 125 9700 -2066.3288 0.059 125 opt. precision reduced, optimizing branchlengths:-2066.3288 -> -2066.3288 9800 -2066.3288 0.034 125 9900 -2066.3288 0.034 125 10000 -2066.3288 0.034 125 10100 -2066.3288 0.034 125 10200 -2066.3288 0.034 125 opt. precision reduced, optimizing branchlengths:-2066.3288 -> -2066.3094 10300 -2066.3094 0.010 125 10400 -2066.3093 0.010 125 10500 -2066.3093 0.010 125 10600 -2066.3093 0.010 125 10700 -2066.3093 0.010 125 10800 -2066.3093 0.010 125 10900 -2066.3092 0.010 125 11000 -2066.3092 0.010 125 11100 -2066.3092 0.010 125 11200 -2066.3092 0.010 125 11300 -2066.3092 0.010 125 11400 -2066.3092 0.010 125 11500 -2066.3092 0.010 125 11600 -2066.3092 0.010 125 11700 -2066.3092 0.010 125 11800 -2066.3092 0.010 125 11900 -2066.3083 0.010 125 12000 -2066.3083 0.010 125 12100 -2066.3083 0.010 125 12200 -2066.3081 0.010 125 12300 -2066.3081 0.010 125 12400 -2066.3081 0.010 125 12500 -2066.3081 0.010 125 12600 -2066.3081 0.010 125 12700 -2066.3080 0.010 125 12800 -2066.3080 0.010 125 12900 -2066.3080 0.010 125 13000 -2066.3080 0.010 125 13100 -2066.3079 0.010 125 13200 -2066.3079 0.010 125 13300 -2066.3079 0.010 125 13400 -2066.3079 0.010 125 13500 -2066.3079 0.010 125 13600 -2066.3079 0.010 125 13700 -2066.3079 0.010 125 13800 -2066.3079 0.010 125 13900 -2066.3079 0.010 125 14000 -2066.3079 0.010 125 14100 -2066.3079 0.010 125 14200 -2066.3079 0.010 125 14300 -2066.3079 0.010 125 14400 -2066.3078 0.010 125 14500 -2066.3078 0.010 125 14600 -2066.3078 0.010 125 14700 -2066.3078 0.010 125 14800 -2066.3078 0.010 125 14900 -2066.3078 0.010 125 15000 -2066.3078 0.010 125 15100 -2066.3078 0.010 125 15200 -2066.3078 0.010 125 15300 -2066.3078 0.010 125 15400 -2066.3078 0.010 125 15500 -2066.3078 0.010 125 15600 -2066.3078 0.010 125 15700 -2066.3078 0.010 125 15800 -2066.3078 0.010 125 15900 -2066.3078 0.010 125 16000 -2066.3078 0.010 125 16100 -2066.3078 0.010 125 16200 -2066.3078 0.010 125 16300 -2066.3078 0.010 125 16400 -2066.3078 0.010 125 16500 -2066.3078 0.010 125 16600 -2066.3078 0.010 125 16700 -2066.3078 0.010 125 16800 -2066.3076 0.010 125 16900 -2066.3076 0.010 125 17000 -2066.3076 0.010 125 17100 -2066.3076 0.010 125 17200 -2066.3076 0.010 125 17300 -2066.3075 0.010 125 17400 -2066.3075 0.010 125 17500 -2066.3075 0.010 125 17600 -2066.3075 0.010 125 17700 -2066.3075 0.010 125 17800 -2066.3075 0.010 125 17900 -2066.3075 0.010 125 18000 -2066.3075 0.010 125 18100 -2066.3075 0.010 125 18200 -2066.3075 0.010 125 18300 -2066.3075 0.010 125 18400 -2066.3075 0.010 125 18500 -2066.3075 0.010 125 18600 -2066.3075 0.010 125 18700 -2066.3075 0.010 125 18800 -2066.3075 0.010 125 18900 -2066.3075 0.010 125 19000 -2066.3075 0.010 125 19100 -2066.3075 0.010 125 19200 -2066.3075 0.010 125 19300 -2066.3075 0.010 125 19400 -2066.3075 0.010 125 19500 -2066.3075 0.010 125 19600 -2066.3074 0.010 125 19700 -2066.3074 0.010 125 19800 -2066.3074 0.010 125 19900 -2066.3074 0.010 125 20000 -2066.3074 0.010 125 20100 -2066.3074 0.010 125 20200 -2066.3074 0.010 125 20300 -2066.3074 0.010 125 20400 -2066.3074 0.010 125 20500 -2066.3074 0.010 125 20600 -2066.3074 0.010 125 20700 -2066.3074 0.010 125 20800 -2066.3074 0.010 125 20900 -2066.3074 0.010 125 21000 -2066.3074 0.010 125 21100 -2066.3074 0.010 125 21200 -2066.3074 0.010 125 21300 -2066.3074 0.010 125 21400 -2066.3074 0.010 125 21500 -2066.3074 0.010 125 21600 -2066.3074 0.010 125 21700 -2066.3074 0.010 125 21800 -2066.3074 0.010 125 21900 -2066.3074 0.010 125 22000 -2066.3074 0.010 125 22100 -2066.3074 0.010 125 22200 -2066.3074 0.010 125 22300 -2066.3074 0.010 125 22400 -2066.3074 0.010 125 22500 -2066.3074 0.010 125 22600 -2066.3074 0.010 125 22700 -2066.3074 0.010 125 22800 -2066.3074 0.010 125 22900 -2066.3074 0.010 125 23000 -2066.3074 0.010 125 23100 -2066.3074 0.010 125 23200 -2066.3074 0.010 125 23300 -2066.3074 0.010 125 23400 -2066.3074 0.010 125 23500 -2066.3074 0.010 125 23600 -2066.3074 0.010 125 23700 -2066.3074 0.010 125 23800 -2066.3074 0.010 125 23900 -2066.3074 0.010 125 24000 -2066.3074 0.010 125 24100 -2066.3074 0.010 125 24200 -2066.3074 0.010 125 24300 -2066.3072 0.010 125 24400 -2066.3072 0.010 125 24500 -2066.3072 0.010 125 24600 -2066.3072 0.010 125 24700 -2066.3072 0.010 125 24800 -2066.3072 0.010 125 24900 -2066.3072 0.010 125 25000 -2066.3072 0.010 125 25100 -2066.3072 0.010 125 25200 -2066.3072 0.010 125 25300 -2066.3072 0.010 125 25400 -2066.3072 0.010 125 25500 -2066.3072 0.010 125 25600 -2066.3072 0.010 125 25700 -2066.3072 0.010 125 25800 -2066.3072 0.010 125 25900 -2066.3072 0.010 125 26000 -2066.3072 0.010 125 26100 -2066.3072 0.010 125 26200 -2066.3072 0.010 125 26300 -2066.3072 0.010 125 26400 -2066.3072 0.010 125 26500 -2066.3072 0.010 125 26600 -2066.3072 0.010 125 26700 -2066.3072 0.010 125 26800 -2066.3072 0.010 125 26900 -2066.3072 0.010 125 27000 -2066.3071 0.010 125 27100 -2066.3071 0.010 125 27200 -2066.3071 0.010 125 27300 -2066.3071 0.010 125 27400 -2066.3071 0.010 125 27500 -2066.3071 0.010 125 27600 -2066.3071 0.010 125 27700 -2066.3071 0.010 125 27800 -2066.3071 0.010 125 27900 -2066.3071 0.010 125 28000 -2066.3071 0.010 125 28100 -2066.3071 0.010 125 28200 -2066.3071 0.010 125 28300 -2066.3071 0.010 125 28400 -2066.3071 0.010 125 28500 -2066.3071 0.010 125 28600 -2066.3071 0.010 125 28700 -2066.3071 0.010 125 28800 -2066.3071 0.010 125 28900 -2066.3071 0.010 125 29000 -2066.3071 0.010 125 29100 -2066.3071 0.010 125 29200 -2066.3071 0.010 125 29300 -2066.3071 0.010 125 29400 -2066.3071 0.010 125 29500 -2066.3071 0.010 125 29600 -2066.3071 0.010 125 29700 -2066.3071 0.010 125 29800 -2066.3071 0.010 125 29900 -2066.3071 0.010 125 30000 -2066.3071 0.010 125 30100 -2066.3071 0.010 125 30200 -2066.3071 0.010 125 30300 -2066.3071 0.010 125 Reached termination condition! last topological improvement at gen 125 Improvement over last 500 gen = 0.00000 Current score = -2066.3071 Performing final optimizations... pass 1 : -2066.3071 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 2 : -2066.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 3 : -2066.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 4 : -2066.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 5 : -2066.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 6 : -2066.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 7 : -2066.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 8 : -2066.3069 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 9 : -2066.3069 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 10: -2066.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 11: -2066.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 12: -2066.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) pass 13: -2066.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 equil freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -2066.3068 Time used = 0 hours, 5 minutes and 29 seconds MODEL REPORT - Parameter values are FINAL Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.482, AG = 2.795, AT = 1.497, CG = 0.867, CT = 4.602, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2006 0.2390 0.2833 0.2771 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5273 with an invariant (invariable) site category, proportion estimated 0.1446 Substitution rate categories under this model: rate proportion 0.0000 0.1446 0.0386 0.2139 0.2694 0.2139 0.8392 0.2139 2.8529 0.2139 >>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 2)<<< ####################################################### Completed 2 replicate search(es) (of 2). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -2066.3067 (best) Replicate 2 : -2066.3068 (same topology as 1) Parameter estimates across search replicates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.483 2.797 1.497 0.868 4.605 1.000 0.201 0.239 0.283 0.277 0.530 0.146 rep 2: 1.482 2.795 1.497 0.867 4.602 1.000 0.201 0.239 0.283 0.277 0.527 0.145 Saving tree from best search rep (#1) to bootstrap file garli_run.run00.boot.tre >>>Completed Bootstrap rep 1<<< #######################################################