.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2606_110x1206_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . '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... . 662 patterns found. (out of a total of 1206 sites) . 540 sites without polymorphism (44.78%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29176.8561] [GTR parameters ] . ( 2 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 3 sec) [ -28715.8595] [ 5819] [depth= 1] . ( 4 sec) [ -28708.0409] [ 5821] [depth= 1] . ( 5 sec) [ -28707.5927] [ 5825] [depth= 1] . ( 5 sec) [ -28694.0716] [ 5821] [depth= 1] . ( 5 sec) [ -28691.7304] [ 5825] [depth= 1] . ( 5 sec) [ -28688.9802] [ 5821] [depth= 1] . ( 6 sec) [ -28682.2184] [ 5822] [depth= 1] . ( 7 sec) [ -28672.5091] [ 5820] [depth= 1] . ( 7 sec) [ -28671.2251] [ 5822] [depth= 1] . ( 8 sec) [ -28668.7801] [ 5817] [depth= 1] . ( 8 sec) [ -28661.4356] [ 5821] [depth= 1] . ( 8 sec) [ -28643.9892] [ 5811] [depth= 1] . ( 8 sec) [ -28643.3466] [ 5809] [depth= 1] . ( 9 sec) [ -28635.7137] [ 5810] [depth= 1] . ( 9 sec) [ -28635.4520] [ 5809] [depth= 1] . ( 9 sec) [ -28632.8133] [ 5810] [depth= 1] . ( 10 sec) [ -28623.9398] [ 5809] [depth= 1] . ( 10 sec) [ -28615.5831] [ 5800] [depth= 1] . ( 11 sec) [ -28612.2649] [ 5801] [depth= 1] . ( 11 sec) [ -28610.5012] [ 5807] [depth= 1] . ( 12 sec) [ -28609.9758] [ 5806] [depth= 1] . ( 12 sec) [ -28603.6648] [ 5807] [depth= 3] . ( 12 sec) [ -28601.8152] [ 5818] [depth= 1] . ( 12 sec) [ -28581.8182] [ 5807] [depth= 1] . ( 13 sec) [ -28571.8591] [ 5816] [depth= 1] . ( 13 sec) [ -28553.8675] [ 5807] [depth= 1] . ( 13 sec) [ -28551.9947] [ 5804] [depth= 2] . ( 14 sec) [ -28533.4293] [ 5810] [depth= 2] . ( 14 sec) [ -28505.6528] [ 5800] [depth= 2] . ( 14 sec) [ -28495.1770] [ 5800] [depth= 1] . ( 15 sec) [ -28494.1748] [ 5800] [depth= 1] . ( 15 sec) [ -28483.5667] [ 5798] [depth= 1] . ( 15 sec) [ -28479.6456] [ 5798] [depth= 1] . ( 15 sec) [ -28474.4368] [ 5796] [depth= 2] . ( 16 sec) [ -28472.6709] [ 5794] [depth= 1] . ( 16 sec) [ -28460.7897] [ 5795] [depth= 1] . ( 16 sec) [ -28459.6662] [ 5797] [depth= 1] . ( 16 sec) [ -28453.7020] [ 5792] [depth= 1] . ( 17 sec) [ -28451.1695] [ 5794] [depth= 2] . ( 17 sec) [ -28450.1356] [ 5794] [depth= 1] . ( 17 sec) [ -28448.6354] [ 5794] [depth= 1] . ( 18 sec) [ -28447.5859] [ 5794] [depth= 1] . ( 18 sec) [ -28446.5516] [ 5793] [depth= 1] . ( 19 sec) [ -28444.5669] [ 5791] [depth= 1] . ( 19 sec) [ -28440.7721] [ 5793] [depth= 1] . ( 19 sec) [ -28427.3921] [ 5786] [depth= 3] . ( 20 sec) [ -28423.8219] [ 5789] [depth= 1] . ( 20 sec) [ -28420.9339] [ 5786] [depth= 1] . ( 20 sec) [ -28419.4819] [ 5786] [depth= 1] . ( 20 sec) [ -28416.5696] [ 5786] [depth= 1] . ( 21 sec) [ -28414.8332] [ 5783] [depth= 2] . ( 21 sec) [ -28411.4261] [ 5787] [depth= 2] . ( 21 sec) [ -28411.1316] [ 5785] [depth= 2] . ( 22 sec) [ -28408.4249] [ 5786] [depth= 1] . ( 22 sec) [ -28405.7013] [ 5784] [depth= 1] . ( 23 sec) [ -28404.6278] [ 5783] [depth= 1] . ( 24 sec) [ -28401.5590] [ 5782] [depth= 1] . ( 24 sec) [ -28400.0291] [ 5782] [depth= 1] . ( 24 sec) [ -28397.2025] [ 5781] [depth= 1] . ( 25 sec) [ -28395.6180] [ 5781] [depth= 1] . ( 25 sec) [ -28391.5621] [ 5780] [depth= 3] . ( 27 sec) [ -28391.5468] [ 5780] [depth= 1] . ( 28 sec) [ -28291.5980] [Branch lengths ] . ( 36 sec) [ -27082.2092] [GTR parameters ] . ( 36 sec) [ -27013.3340] [Alpha ][ 0.333749] . ( 39 sec) [ -27012.2648] [ 5782] [depth= 1] . ( 41 sec) [ -27011.5357] [ 5783] [depth= 1] . ( 42 sec) [ -27004.5047] [ 5781] [depth= 2] . ( 42 sec) [ -27003.2965] [ 5782] [depth= 1] . ( 43 sec) [ -27001.5368] [ 5784] [depth= 1] . ( 44 sec) [ -27001.3865] [ 5787] [depth= 1] . ( 46 sec) [ -26991.5026] [ 5789] [depth= 1] . ( 47 sec) [ -26990.4611] [ 5790] [depth= 1] . ( 47 sec) [ -26988.0677] [ 5791] [depth= 1] . ( 47 sec) [ -26987.1500] [ 5791] [depth= 1] . ( 48 sec) [ -26986.8617] [ 5790] [depth= 1] . ( 57 sec) [ -26964.1626] [Branch lengths ] . ( 63 sec) [ -26962.1602] [GTR parameters ] . ( 63 sec) [ -26961.4357] [Alpha ][ 0.320270] . ( 68 sec) [ -26960.9723] [ 5789] [depth= 1] . ( 70 sec) [ -26960.9303] [ 5786] [depth= 1] . ( 85 sec) [ -26958.5358] [Branch lengths ] . ( 89 sec) [ -26958.4968] [GTR parameters ] . ( 90 sec) [ -26958.2739] [Alpha ][ 0.313079] . ( 128 sec) [ -26957.8990] [Branch lengths ] . ( 217 sec) [ -26955.9485] [ 5792] [depth= 3] . ( 247 sec) [ -26955.7805] [ 5795] [depth= 1] . ( 248 sec) [ -26950.7261] [ 5793] [depth= 1] . ( 395 sec) [ -26948.1296] [Branch lengths ] . ( 403 sec) [ -26947.9890] [GTR parameters ] . ( 403 sec) [ -26947.8141] [Alpha ][ 0.306527] . ( 624 sec) [ -26947.5941] [Branch lengths ] . ( 624 sec) [ -26947.5941] [Topology ] . ( 629 sec) [ -26947.3041] [Topology ] . ( 634 sec) [ -26946.8506] [Topology ] . ( 638 sec) [ -26946.6519] [Topology ] . ( 643 sec) [ -26946.6088] [Topology ] . ( 648 sec) [ -26946.5940] [Topology ] . ( 653 sec) [ -26946.5885] [Topology ] . ( 658 sec) [ -26946.5863] [Topology ] . ( 663 sec) [ -26946.5855] [Topology ] . ( 670 sec) [ -26946.5762] [GTR parameters ] . ( 670 sec) [ -26946.4987] [Alpha ][ 0.302203] . ( 670 sec) [ -26946.4987] [Topology ] . ( 675 sec) [ -26946.4689] [Topology ] . ( 680 sec) [ -26946.4599] [Topology ] . ( 685 sec) [ -26946.4568] [Topology ] . ( 690 sec) [ -26946.4557] [Topology ] . ( 694 sec) [ -26946.4553] [Topology ] . ( 700 sec) [ -26946.4538] [GTR parameters ] . ( 700 sec) [ -26946.4346] [Alpha ][ 0.300059] . ( 700 sec) [ -26946.4346] [Topology ] . ( 705 sec) [ -26946.4260] [Topology ] . ( 710 sec) [ -26946.4234] [Topology ] . ( 715 sec) [ -26946.4225] [Topology ] . ( 717 sec) [ -26946.4224] [GTR parameters ] . ( 717 sec) [ -26946.4187] [Alpha ][ 0.299097] . ( 717 sec) [ -26946.4187] [Topology ] . ( 722 sec) [ -26946.4156] [Topology ] . ( 727 sec) [ -26946.4146] [Topology ] . ( 732 sec) [ -26946.4136] [GTR parameters ] . ( 732 sec) [ -26946.4123] [Alpha ][ 0.298523] . ( 732 sec) [ -26946.4123] [Topology ] . ( 737 sec) [ -26946.4108] [Topology ] . ( 742 sec) [ -26946.4104] [Topology ] . ( 743 sec) [ -26946.4103] [GTR parameters ] . ( 744 sec) [ -26946.4099] [Alpha ][ 0.298200] . ( 744 sec) [ -26946.4099] [Topology ] . ( 748 sec) [ -26946.4093] [Topology ] . ( 750 sec) [ -26946.4093] [GTR parameters ] . ( 751 sec) [ -26946.4093] [Alpha ][ 0.298200] . Checking for NNIs, optimizing five branches... . ( 786 sec) [ -26946.1516] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26946.151631. . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Time used 0h13m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 515.64user 0.00system 13:45.43elapsed 62%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps