Running serial GARLI, version 0.96beta8 (April 2008) This version has undergone much testing, but is still a BETA VERSION. - Please check results carefully! - Compiled Oct 22 2008 11:43:21 using GNU gcc compiler version 3.2.3 Using NCL version 2.1.00 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. 125 parsimony-informative characters. 48 autapomorphic 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)** >>>Search rep 1 (of 2)<<< 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=18598 creating random starting tree... Initial ln Likelihood: -2763.4936 optimizing starting branch lengths and rate heterogeneity parameters... pass 1 : + 266.5991 (branch= 263.34 scale= 0.67 alpha= 2.59 pinv= 0.00) pass 2 : + 24.8278 (branch= 24.83 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 3 : + 4.9122 (branch= 4.12 scale= 0.80 alpha= 0.00 pinv= 0.00) pass 4 : + 0.5510 (branch= 0.55 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 5 : + 0.0000 (branch= 0.00 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -2466.6034 gen current_lnL precision last_tree_imp 0 -2466.6034 0.500 0 100 -2176.0506 0.500 78 200 -2173.2622 0.500 193 300 -2172.0563 0.500 193 400 -2170.5281 0.500 193 500 -2168.1381 0.500 193 600 -2167.2867 0.500 193 700 -2165.2177 0.500 193 opt. precision reduced, optimizing branchlengths:-2165.2177 -> -2165.2140 800 -2164.9805 0.475 193 900 -2163.6736 0.475 193 1000 -2162.9132 0.475 193 1100 -2162.1988 0.475 193 1200 -2162.0164 0.475 193 opt. precision reduced, optimizing branchlengths:-2162.0164 -> -2162.0164 1300 -2161.1915 0.451 193 1400 -2160.3882 0.451 193 1500 -2159.8847 0.451 193 1600 -2159.7882 0.451 193 1700 -2159.2471 0.451 193 opt. precision reduced, optimizing branchlengths:-2159.2471 -> -2159.2450 1800 -2159.1267 0.426 193 1900 -2158.6318 0.426 193 2000 -2158.4406 0.426 193 2100 -2158.3256 0.426 193 2200 -2157.6118 0.426 193 opt. precision reduced, optimizing branchlengths:-2157.6118 -> -2157.6118 2300 -2157.4153 0.402 193 2400 -2157.4080 0.402 193 2500 -2157.2908 0.402 193 2600 -2157.0492 0.402 193 2700 -2156.9184 0.402 193 opt. precision reduced, optimizing branchlengths:-2156.9184 -> -2156.9184 2800 -2156.7452 0.377 193 2900 -2156.6837 0.377 193 3000 -2156.5610 0.377 193 3100 -2156.5443 0.377 193 3200 -2156.4943 0.377 193 opt. precision reduced, optimizing branchlengths:-2156.4943 -> -2156.4943 3300 -2156.4887 0.353 193 3400 -2156.4621 0.353 193 3500 -2156.4471 0.353 193 3600 -2156.4445 0.353 193 3700 -2156.4405 0.353 193 opt. precision reduced, optimizing branchlengths:-2156.4405 -> -2156.4405 3800 -2156.4399 0.328 193 3900 -2156.4007 0.328 193 4000 -2156.3939 0.328 193 4100 -2156.3900 0.328 193 4200 -2156.3820 0.328 193 opt. precision reduced, optimizing branchlengths:-2156.3820 -> -2156.3820 4300 -2156.3784 0.304 193 4400 -2156.3769 0.304 193 4500 -2156.3712 0.304 193 4600 -2156.3710 0.304 193 4700 -2156.3696 0.304 193 opt. precision reduced, optimizing branchlengths:-2156.3696 -> -2156.3696 4800 -2156.3685 0.279 193 4900 -2156.3570 0.279 193 5000 -2156.3477 0.279 193 5100 -2156.3465 0.279 193 5200 -2156.3452 0.279 193 opt. precision reduced, optimizing branchlengths:-2156.3452 -> -2156.3452 5300 -2156.3445 0.255 193 5400 -2156.3445 0.255 193 5500 -2156.3445 0.255 193 5600 -2156.3436 0.255 193 5700 -2156.3423 0.255 193 opt. precision reduced, optimizing branchlengths:-2156.3423 -> -2156.3423 5800 -2156.3401 0.230 193 5900 -2156.3370 0.230 193 6000 -2156.3370 0.230 193 6100 -2156.3357 0.230 193 6200 -2156.3346 0.230 193 opt. precision reduced, optimizing branchlengths:-2156.3346 -> -2156.3346 6300 -2156.3346 0.206 193 6400 -2156.3310 0.206 193 6500 -2156.3306 0.206 193 6600 -2156.3294 0.206 193 6700 -2156.3292 0.206 193 opt. precision reduced, optimizing branchlengths:-2156.3292 -> -2156.3292 6800 -2156.3292 0.181 193 6900 -2156.3290 0.181 193 7000 -2156.3290 0.181 193 7100 -2156.3270 0.181 193 7200 -2156.3270 0.181 193 opt. precision reduced, optimizing branchlengths:-2156.3270 -> -2156.3270 7300 -2156.3270 0.157 193 7400 -2156.3270 0.157 193 7500 -2156.3183 0.157 193 7600 -2156.3182 0.157 193 7700 -2156.3178 0.157 193 opt. precision reduced, optimizing branchlengths:-2156.3178 -> -2156.3178 7800 -2156.3178 0.132 193 7900 -2156.3178 0.132 193 8000 -2156.3178 0.132 193 8100 -2156.3178 0.132 193 8200 -2156.3176 0.132 193 opt. precision reduced, optimizing branchlengths:-2156.3176 -> -2156.3176 8300 -2156.3171 0.108 193 8400 -2156.3166 0.108 193 8500 -2156.3150 0.108 193 8600 -2156.3150 0.108 193 8700 -2156.3150 0.108 193 opt. precision reduced, optimizing branchlengths:-2156.3150 -> -2156.3150 8800 -2156.3148 0.083 193 8900 -2156.3136 0.083 193 9000 -2156.3128 0.083 193 9100 -2156.3128 0.083 193 9200 -2156.3127 0.083 193 opt. precision reduced, optimizing branchlengths:-2156.3127 -> -2156.3127 9300 -2156.3127 0.059 193 9400 -2156.3125 0.059 193 9500 -2156.3125 0.059 193 9600 -2156.3122 0.059 193 9700 -2156.3112 0.059 193 opt. precision reduced, optimizing branchlengths:-2156.3112 -> -2156.3112 9800 -2156.3112 0.034 193 9900 -2156.3107 0.034 193 10000 -2156.3107 0.034 193 10100 -2156.3102 0.034 193 10200 -2156.3073 0.034 193 opt. precision reduced, optimizing branchlengths:-2156.3073 -> -2156.2910 10300 -2156.2910 0.010 193 10400 -2156.2910 0.010 193 10500 -2156.2877 0.010 193 10600 -2156.2877 0.010 193 10700 -2156.2877 0.010 193 10800 -2156.2877 0.010 193 10900 -2156.2842 0.010 193 11000 -2156.2830 0.010 193 11100 -2156.2830 0.010 193 11200 -2156.2830 0.010 193 11300 -2156.2830 0.010 193 11400 -2156.2826 0.010 193 11500 -2156.2803 0.010 193 11600 -2156.2785 0.010 193 11700 -2156.2784 0.010 193 11800 -2156.2784 0.010 193 11900 -2156.2781 0.010 193 12000 -2156.2781 0.010 193 12100 -2156.2739 0.010 193 12200 -2156.2736 0.010 193 12300 -2156.2732 0.010 193 12400 -2156.2732 0.010 193 12500 -2156.2732 0.010 193 12600 -2156.2732 0.010 193 12700 -2156.2732 0.010 193 12800 -2156.2732 0.010 193 12900 -2156.2720 0.010 193 13000 -2156.2720 0.010 193 13100 -2156.2720 0.010 193 13200 -2156.2720 0.010 193 13300 -2156.2720 0.010 193 13400 -2156.2719 0.010 193 13500 -2156.2718 0.010 193 13600 -2156.2688 0.010 193 13700 -2156.2687 0.010 193 13800 -2156.2660 0.010 193 13900 -2156.2643 0.010 193 14000 -2156.2643 0.010 193 14100 -2156.2643 0.010 193 14200 -2156.2632 0.010 193 14300 -2156.2621 0.010 193 14400 -2156.2621 0.010 193 14500 -2156.2611 0.010 193 14600 -2156.2597 0.010 193 14700 -2156.2596 0.010 193 14800 -2156.2590 0.010 193 14900 -2156.2590 0.010 193 15000 -2156.2589 0.010 193 15100 -2156.2589 0.010 193 15200 -2156.2588 0.010 193 15300 -2156.2588 0.010 193 15400 -2156.2587 0.010 193 15500 -2156.2587 0.010 193 15600 -2156.2587 0.010 193 15700 -2156.2587 0.010 193 15800 -2156.2563 0.010 193 15900 -2156.2563 0.010 193 16000 -2156.2562 0.010 193 16100 -2156.2548 0.010 193 16200 -2156.2548 0.010 193 16300 -2156.2544 0.010 193 16400 -2156.2520 0.010 193 16500 -2156.2520 0.010 193 16600 -2156.2498 0.010 193 16700 -2156.2498 0.010 193 16800 -2156.2498 0.010 193 16900 -2156.2492 0.010 193 17000 -2156.2488 0.010 193 17100 -2156.2474 0.010 193 17200 -2156.2474 0.010 193 17300 -2156.2474 0.010 193 17400 -2156.2469 0.010 193 17500 -2156.2469 0.010 193 17600 -2156.2466 0.010 193 17700 -2156.2456 0.010 193 17800 -2156.2456 0.010 193 17900 -2156.2456 0.010 193 18000 -2156.2456 0.010 193 18100 -2156.2452 0.010 193 18200 -2156.2452 0.010 193 18300 -2156.2450 0.010 193 18400 -2156.2450 0.010 193 18500 -2156.2450 0.010 193 18600 -2156.2450 0.010 193 18700 -2156.2449 0.010 193 18800 -2156.2432 0.010 193 18900 -2156.2416 0.010 193 19000 -2156.2408 0.010 193 19100 -2156.2408 0.010 193 19200 -2156.2407 0.010 193 19300 -2156.2406 0.010 193 19400 -2156.2406 0.010 193 19500 -2156.2406 0.010 193 19600 -2156.2406 0.010 193 19700 -2156.2406 0.010 193 19800 -2156.2400 0.010 193 19900 -2156.2400 0.010 193 20000 -2156.2400 0.010 193 20100 -2156.2400 0.010 193 20200 -2156.2400 0.010 193 20300 -2156.2400 0.010 193 Reached termination condition! last topological improvement at gen 193 Improvement over last 500 gen = 0.00001 Current score = -2156.2400 Performing final branch optimization... pass 1 -2156.2400 pass 2 -2156.2400 pass 3 -2156.2400 pass 4 -2156.2400 pass 5 -2156.2400 pass 6 -2156.2398 pass 7 -2156.2398 pass 8 -2156.2395 pass 9 -2156.2393 pass 10 -2156.2393 pass 11 -2156.2393 Final score = -2156.2393 Time used so far = 0 hours, 1 minutes and 15 seconds finished >>>Completed Search rep 1 (of 2)<<< MODEL REPORT - Parameter values are FINAL Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.067, AG = 2.792, AT = 1.631, CG = 1.147, CT = 4.692, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2011 0.2633 0.2960 0.2396 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4381 with an invariant (invariable) site category, proportion estimated 0.0302 Substitution rate categories under this model: rate proportion 0.0000 0.0302 0.0226 0.2425 0.2096 0.2425 0.7694 0.2425 2.9984 0.2425 >>>Search rep 2 (of 2)<<< 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=877821914 creating random starting tree... Initial ln Likelihood: -2805.0675 optimizing starting branch lengths and rate heterogeneity parameters... pass 1 : + 370.4708 (branch= 367.71 scale= 0.00 alpha= 2.76 pinv= 0.00) pass 2 : + 40.6719 (branch= 39.89 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 3 : + 0.6057 (branch= 0.61 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 4 : + 0.0000 (branch= 0.00 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -2393.3191 gen current_lnL precision last_tree_imp 0 -2393.3191 0.500 0 100 -2181.4934 0.500 99 200 -2177.1960 0.500 111 300 -2175.3782 0.500 111 400 -2171.7822 0.500 111 500 -2170.3470 0.500 111 600 -2169.4683 0.500 111 700 -2168.6168 0.500 111 opt. precision reduced, optimizing branchlengths:-2168.6168 -> -2168.6168 800 -2167.6811 0.475 111 900 -2166.4916 0.475 111 1000 -2165.7590 0.475 111 1100 -2165.2121 0.475 111 1200 -2164.2785 0.475 111 opt. precision reduced, optimizing branchlengths:-2164.2785 -> -2164.2785 1300 -2164.1014 0.451 111 1400 -2163.8311 0.451 111 1500 -2163.3830 0.451 111 1600 -2162.8792 0.451 111 1700 -2162.5384 0.451 111 opt. precision reduced, optimizing branchlengths:-2162.5384 -> -2162.5384 1800 -2161.8029 0.426 111 1900 -2161.5721 0.426 111 2000 -2160.0536 0.426 111 2100 -2159.8308 0.426 111 2200 -2159.6762 0.426 111 opt. precision reduced, optimizing branchlengths:-2159.6762 -> -2159.6762 2300 -2159.3236 0.402 111 2400 -2158.9721 0.402 111 2500 -2158.6902 0.402 111 2600 -2158.3918 0.402 111 2700 -2158.2120 0.402 111 opt. precision reduced, optimizing branchlengths:-2158.2120 -> -2158.2120 2800 -2158.1672 0.377 111 2900 -2158.0950 0.377 111 3000 -2157.6850 0.377 111 3100 -2157.5105 0.377 111 3200 -2157.5045 0.377 111 opt. precision reduced, optimizing branchlengths:-2157.5045 -> -2157.5045 3300 -2157.4926 0.353 111 3400 -2157.4669 0.353 111 3500 -2157.4668 0.353 111 3600 -2157.4477 0.353 111 3700 -2157.4434 0.353 111 opt. precision reduced, optimizing branchlengths:-2157.4434 -> -2157.4434 3800 -2157.4194 0.328 111 3900 -2157.4082 0.328 111 4000 -2157.3989 0.328 111 4100 -2157.3893 0.328 111 4200 -2157.3765 0.328 111 opt. precision reduced, optimizing branchlengths:-2157.3765 -> -2157.3765 4300 -2157.3752 0.304 111 4400 -2157.3714 0.304 111 4500 -2157.3582 0.304 111 4600 -2157.3416 0.304 111 4700 -2157.1437 0.304 111 opt. precision reduced, optimizing branchlengths:-2157.1437 -> -2157.1437 4800 -2156.9759 0.279 111 4900 -2156.8182 0.279 111 5000 -2156.7509 0.279 111 5100 -2156.6584 0.279 111 5200 -2156.5713 0.279 111 opt. precision reduced, optimizing branchlengths:-2156.5713 -> -2156.5713 5300 -2156.5344 0.255 111 5400 -2156.4748 0.255 111 5500 -2156.4441 0.255 111 5600 -2156.4131 0.255 111 5700 -2156.4086 0.255 111 opt. precision reduced, optimizing branchlengths:-2156.4086 -> -2156.4086 5800 -2156.4027 0.230 111 5900 -2156.3964 0.230 111 6000 -2156.3858 0.230 111 6100 -2156.3749 0.230 111 6200 -2156.3647 0.230 111 opt. precision reduced, optimizing branchlengths:-2156.3647 -> -2156.3647 6300 -2156.3647 0.206 111 6400 -2156.3647 0.206 111 6500 -2156.3603 0.206 111 6600 -2156.3579 0.206 111 6700 -2156.3522 0.206 111 opt. precision reduced, optimizing branchlengths:-2156.3522 -> -2156.3522 6800 -2156.3464 0.181 111 6900 -2156.3464 0.181 111 7000 -2156.3444 0.181 111 7100 -2156.3428 0.181 111 7200 -2156.3360 0.181 111 opt. precision reduced, optimizing branchlengths:-2156.3360 -> -2156.3360 7300 -2156.3305 0.157 111 7400 -2156.3305 0.157 111 7500 -2156.3288 0.157 111 7600 -2156.3227 0.157 111 7700 -2156.3197 0.157 111 opt. precision reduced, optimizing branchlengths:-2156.3197 -> -2156.3197 7800 -2156.3166 0.132 111 7900 -2156.3122 0.132 111 8000 -2156.3116 0.132 111 8100 -2156.3109 0.132 111 8200 -2156.3095 0.132 111 opt. precision reduced, optimizing branchlengths:-2156.3095 -> -2156.3095 8300 -2156.3087 0.108 111 8400 -2156.3080 0.108 111 8500 -2156.3055 0.108 111 8600 -2156.3021 0.108 111 8700 -2156.3014 0.108 111 opt. precision reduced, optimizing branchlengths:-2156.3014 -> -2156.3014 8800 -2156.2999 0.083 111 8900 -2156.2999 0.083 111 9000 -2156.2980 0.083 111 9100 -2156.2977 0.083 111 9200 -2156.2966 0.083 111 opt. precision reduced, optimizing branchlengths:-2156.2966 -> -2156.2966 9300 -2156.2959 0.059 111 9400 -2156.2950 0.059 111 9500 -2156.2923 0.059 111 9600 -2156.2923 0.059 111 9700 -2156.2899 0.059 111 opt. precision reduced, optimizing branchlengths:-2156.2899 -> -2156.2899 9800 -2156.2899 0.034 111 9900 -2156.2899 0.034 111 10000 -2156.2899 0.034 111 10100 -2156.2892 0.034 111 10200 -2156.2890 0.034 111 opt. precision reduced, optimizing branchlengths:-2156.2890 -> -2156.2691 10300 -2156.2689 0.010 111 10400 -2156.2689 0.010 111 10500 -2156.2684 0.010 111 10600 -2156.2684 0.010 111 10700 -2156.2684 0.010 111 10800 -2156.2680 0.010 111 10900 -2156.2678 0.010 111 11000 -2156.2678 0.010 111 11100 -2156.2678 0.010 111 11200 -2156.2676 0.010 111 11300 -2156.2676 0.010 111 11400 -2156.2676 0.010 111 11500 -2156.2676 0.010 111 11600 -2156.2676 0.010 111 11700 -2156.2676 0.010 111 11800 -2156.2673 0.010 111 11900 -2156.2673 0.010 111 12000 -2156.2665 0.010 111 12100 -2156.2665 0.010 111 12200 -2156.2665 0.010 111 12300 -2156.2665 0.010 111 12400 -2156.2665 0.010 111 12500 -2156.2662 0.010 111 12600 -2156.2661 0.010 111 12700 -2156.2661 0.010 111 12800 -2156.2656 0.010 111 12900 -2156.2655 0.010 111 13000 -2156.2655 0.010 111 13100 -2156.2626 0.010 111 13200 -2156.2626 0.010 111 13300 -2156.2620 0.010 111 13400 -2156.2620 0.010 111 13500 -2156.2619 0.010 111 13600 -2156.2619 0.010 111 13700 -2156.2619 0.010 111 13800 -2156.2561 0.010 111 13900 -2156.2558 0.010 111 14000 -2156.2533 0.010 111 14100 -2156.2533 0.010 111 14200 -2156.2533 0.010 111 14300 -2156.2533 0.010 111 14400 -2156.2525 0.010 111 14500 -2156.2511 0.010 111 14600 -2156.2503 0.010 111 14700 -2156.2503 0.010 111 14800 -2156.2495 0.010 111 14900 -2156.2487 0.010 111 15000 -2156.2487 0.010 111 15100 -2156.2487 0.010 111 15200 -2156.2487 0.010 111 15300 -2156.2487 0.010 111 15400 -2156.2487 0.010 111 15500 -2156.2487 0.010 111 15600 -2156.2487 0.010 111 15700 -2156.2487 0.010 111 15800 -2156.2487 0.010 111 15900 -2156.2487 0.010 111 16000 -2156.2487 0.010 111 16100 -2156.2487 0.010 111 16200 -2156.2486 0.010 111 16300 -2156.2486 0.010 111 16400 -2156.2486 0.010 111 16500 -2156.2475 0.010 111 16600 -2156.2473 0.010 111 16700 -2156.2473 0.010 111 16800 -2156.2473 0.010 111 16900 -2156.2472 0.010 111 17000 -2156.2470 0.010 111 17100 -2156.2470 0.010 111 17200 -2156.2470 0.010 111 17300 -2156.2455 0.010 111 17400 -2156.2454 0.010 111 17500 -2156.2423 0.010 111 17600 -2156.2423 0.010 111 17700 -2156.2389 0.010 111 17800 -2156.2389 0.010 111 17900 -2156.2378 0.010 111 18000 -2156.2378 0.010 111 18100 -2156.2378 0.010 111 18200 -2156.2373 0.010 111 18300 -2156.2370 0.010 111 18400 -2156.2369 0.010 111 18500 -2156.2369 0.010 111 18600 -2156.2369 0.010 111 18700 -2156.2369 0.010 111 18800 -2156.2357 0.010 111 18900 -2156.2341 0.010 111 19000 -2156.2319 0.010 111 19100 -2156.2314 0.010 111 19200 -2156.2313 0.010 111 19300 -2156.2313 0.010 111 19400 -2156.2304 0.010 111 19500 -2156.2304 0.010 111 19600 -2156.2304 0.010 111 19700 -2156.2302 0.010 111 19800 -2156.2302 0.010 111 19900 -2156.2302 0.010 111 20000 -2156.2302 0.010 111 20100 -2156.2294 0.010 111 20200 -2156.2287 0.010 111 20300 -2156.2283 0.010 111 Reached termination condition! last topological improvement at gen 111 Improvement over last 500 gen = 0.00191 Current score = -2156.2283 Performing final branch optimization... pass 1 -2156.2283 pass 2 -2156.2283 pass 3 -2156.2283 pass 4 -2156.2283 pass 5 -2156.2283 pass 6 -2156.2281 pass 7 -2156.2279 pass 8 -2156.2275 pass 9 -2156.2275 pass 10 -2156.2275 pass 11 -2156.2274 Final score = -2156.2274 Time used = 0 hours, 2 minutes and 51 seconds finished >>>Completed Search rep 2 (of 2)<<< MODEL REPORT - Parameter values are FINAL Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.072, AG = 2.799, AT = 1.637, CG = 1.148, CT = 4.699, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2009 0.2635 0.2960 0.2396 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4271 with an invariant (invariable) site category, proportion estimated 0.0213 Substitution rate categories under this model: rate proportion 0.0000 0.0213 0.0208 0.2447 0.2017 0.2447 0.7590 0.2447 3.0185 0.2447 Completed 2 replicate runs (of 2). Results: Replicate 1 : -2156.2393 Replicate 2 : -2156.2274 (best) (same topology as 1) Final result of the best scoring rep (#2) stored in garli_run.best.tre Final results of all reps stored in garli_run.best.all.tre