.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2928_81x1651_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 507 patterns found. (out of a total of 1651 sites) . 1189 sites without polymorphism (72.02%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6807.1927] [Ts/ts ratio ][ 20.501310] . ( 0 sec) [ -6806.6217] [ 888] [depth= 1] . ( 0 sec) [ -6806.3021] [ 888] [depth= 1] . ( 1 sec) [ -6806.0350] [ 888] [depth= 3] . ( 1 sec) [ -6805.8275] [ 888] [depth= 2] . ( 1 sec) [ -6805.4284] [ 888] [depth= 2] . ( 2 sec) [ -6805.3420] [ 888] [depth= 3] . ( 2 sec) [ -6805.2934] [ 888] [depth= 1] . ( 2 sec) [ -6805.2579] [ 888] [depth= 3] . ( 2 sec) [ -6805.2415] [ 888] [depth= 1] . ( 3 sec) [ -6805.2160] [ 888] [depth= 2] . ( 3 sec) [ -6805.2048] [ 888] [depth= 1] . ( 4 sec) [ -6804.2507] [ 888] [depth= 1] . ( 4 sec) [ -6804.1046] [ 888] [depth= 1] . ( 4 sec) [ -6804.0112] [ 888] [depth= 1] . ( 4 sec) [ -6803.7217] [ 888] [depth= 1] . ( 4 sec) [ -6803.5443] [ 888] [depth= 2] . ( 4 sec) [ -6802.5332] [ 888] [depth= 1] . ( 5 sec) [ -6800.9601] [ 889] [depth= 1] . ( 6 sec) [ -6800.8979] [ 893] [depth= 1] . ( 6 sec) [ -6800.2561] [ 892] [depth= 1] . ( 6 sec) [ -6799.2684] [ 890] [depth= 1] . ( 6 sec) [ -6778.8797] [ 887] [depth= 1] . ( 6 sec) [ -6777.0886] [ 889] [depth= 1] . ( 7 sec) [ -6777.0524] [ 889] [depth= 1] . ( 7 sec) [ -6775.7516] [ 889] [depth= 2] . ( 7 sec) [ -6775.6200] [ 889] [depth= 1] . ( 7 sec) [ -6775.4824] [ 889] [depth= 2] . ( 7 sec) [ -6775.4634] [ 889] [depth= 3] . ( 7 sec) [ -6769.3291] [ 889] [depth= 1] . ( 8 sec) [ -6765.8657] [ 889] [depth= 1] . ( 8 sec) [ -6765.7172] [ 889] [depth= 5] . ( 8 sec) [ -6765.5716] [ 889] [depth= 1] . ( 9 sec) [ -6765.2802] [ 889] [depth= 1] . ( 9 sec) [ -6765.2129] [ 889] [depth= 7] . ( 9 sec) [ -6765.0514] [ 889] [depth= 6] . ( 9 sec) [ -6764.5444] [ 889] [depth= 2] . ( 9 sec) [ -6764.3119] [ 889] [depth= 6] . ( 9 sec) [ -6764.1362] [ 889] [depth= 5] . ( 10 sec) [ -6764.0527] [ 889] [depth= 4] . ( 10 sec) [ -6763.9378] [ 889] [depth= 4] . ( 11 sec) [ -6763.8529] [ 889] [depth= 1] . ( 12 sec) [ -6763.5366] [ 889] [depth= 1] . ( 12 sec) [ -6763.2889] [ 889] [depth= 1] . ( 14 sec) [ -6763.0559] [ 889] [depth= 2] . ( 14 sec) [ -6763.0424] [ 889] [depth= 4] . ( 15 sec) [ -6762.8896] [ 889] [depth= 2] . ( 18 sec) [ -6759.9602] [ 890] [depth= 1] . ( 19 sec) [ -6759.6114] [ 889] [depth= 1] . ( 19 sec) [ -6758.6201] [ 890] [depth= 1] . ( 22 sec) [ -6758.6097] [ 890] [depth= 1] . ( 24 sec) [ -6757.8888] [ 890] [depth= 1] . ( 24 sec) [ -6757.1459] [ 889] [depth= 3] . ( 24 sec) [ -6757.1331] [ 890] [depth= 1] . ( 25 sec) [ -6756.7574] [ 889] [depth= 1] . ( 25 sec) [ -6756.6969] [ 889] [depth= 1] . ( 25 sec) [ -6756.6512] [ 889] [depth= 2] . ( 26 sec) [ -6756.5645] [ 890] [depth= 1] . ( 27 sec) [ -6756.5541] [ 890] [depth= 1] . ( 35 sec) [ -6741.7165] [Branch lengths ] . ( 35 sec) [ -6741.5842] [Ts/ts ratio ][ 21.708004] . ( 40 sec) [ -6740.3383] [ 889] [depth= 1] . ( 40 sec) [ -6739.9726] [ 887] [depth= 1] . ( 40 sec) [ -6739.5004] [ 889] [depth= 1] . ( 40 sec) [ -6739.4672] [ 889] [depth= 1] . ( 41 sec) [ -6739.3550] [ 889] [depth= 1] . ( 45 sec) [ -6739.3398] [ 889] [depth= 2] . ( 79 sec) [ -6737.1663] [Branch lengths ] . ( 79 sec) [ -6737.1661] [Ts/ts ratio ][ 21.765108] . ( 121 sec) [ -6737.1028] [Branch lengths ] . ( 187 sec) [ -6737.1007] [Branch lengths ] . ( 187 sec) [ -6737.1007] [Topology ] . ( 188 sec) [ -6737.1005] [Topology ] . ( 188 sec) [ -6737.1004] [Ts/ts ratio ][ 21.798607] . Checking for NNIs, optimizing five branches... . ( 198 sec) [ -6737.0945] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6737.094461. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 376.546137 1.000000 0.107690 100 82.577840 1.000000 0.034181 97 19.927892 0.954000 0.008143 56 5.278272 0.677000 0.009434 47 5.703548 0.844000 0.007533 100 266.572482 1.000000 0.068216 61 1.106155 0.227000 0.004233 100 213.930147 1.000000 0.038158 98 24.858222 0.960000 0.008827 53 1.046239 0.738000 0.001177 6 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 50 1.439215 0.314000 0.002460 100 279.939079 1.000000 0.035645 32 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 51 5.448527 0.811000 0.002798 100 79.853453 0.996000 0.013032 99 67.620511 0.994000 0.013594 100 135.895022 1.000000 0.020178 43 -1.000000 0.000000 0.000000 72 3.105525 0.792000 0.002906 100 122.341202 0.999000 0.021489 100 98.592901 0.999000 0.016887 100 31.685440 0.984000 0.006533 98 44.911739 0.988000 0.013802 71 4.799505 0.766000 0.004620 100 197.910673 1.000000 0.037983 67 2.479705 0.755000 0.000779 98 35.033977 0.979000 0.008519 74 2.598033 0.699000 0.001386 100 81.737825 0.999000 0.009941 68 7.148897 0.728000 0.000734 9 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 100 62.891545 0.996000 0.008987 61 7.129548 0.826000 0.000674 5 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 67 14.796178 0.910000 0.000674 2 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 100 36.459343 0.977000 0.007307 100 73.499100 0.996000 0.012698 100 106.468352 1.000000 0.013804 52 8.964539 0.878000 0.001394 14 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 18 0.188543 0.000000 0.000644 60 20.334966 0.856000 0.002953 17 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 85 23.672025 0.929000 0.001356 . Printing the most likely tree in file 'nucleic_M2928_81x1651_2006.phy_phyml_tree.txt'... . Time used 4h32m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo