.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 935 patterns found. (out of a total of 1271 sites) . 411 sites without polymorphism (32.34%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -36495.9506] [GTR parameters ] . ( 5 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 7 sec) [ -35998.6346] [ 9298] [depth= 1] . ( 9 sec) [ -35996.9518] [ 9294] [depth= 1] . ( 9 sec) [ -35995.6249] [ 9299] [depth= 2] . ( 11 sec) [ -35994.7713] [ 9302] [depth= 1] . ( 11 sec) [ -35981.7535] [ 9299] [depth= 1] . ( 11 sec) [ -35976.0490] [ 9316] [depth= 1] . ( 11 sec) [ -35945.9384] [ 9299] [depth= 1] . ( 11 sec) [ -35899.7875] [ 9305] [depth= 1] . ( 12 sec) [ -35892.5708] [ 9304] [depth= 1] . ( 12 sec) [ -35889.1581] [ 9301] [depth= 1] . ( 12 sec) [ -35884.2421] [ 9304] [depth= 1] . ( 12 sec) [ -35877.1616] [ 9301] [depth= 1] . ( 13 sec) [ -35873.8010] [ 9309] [depth= 1] . ( 13 sec) [ -35869.5312] [ 9309] [depth= 1] . ( 13 sec) [ -35862.6503] [ 9309] [depth= 1] . ( 13 sec) [ -35862.3070] [ 9317] [depth= 2] . ( 13 sec) [ -35857.7687] [ 9312] [depth= 1] . ( 14 sec) [ -35848.4448] [ 9312] [depth= 2] . ( 15 sec) [ -35827.9825] [ 9338] [depth= 1] . ( 15 sec) [ -35788.5061] [ 9312] [depth= 1] . ( 15 sec) [ -35773.4592] [ 9315] [depth= 1] . ( 15 sec) [ -35745.6961] [ 9309] [depth= 3] . ( 16 sec) [ -35722.4760] [ 9309] [depth= 1] . ( 17 sec) [ -35717.8663] [ 9309] [depth= 1] . ( 17 sec) [ -35712.9057] [ 9318] [depth= 1] . ( 17 sec) [ -35687.5457] [ 9309] [depth= 1] . ( 18 sec) [ -35680.2336] [ 9304] [depth= 1] . ( 19 sec) [ -35678.5963] [ 9293] [depth= 5] . ( 19 sec) [ -35661.6697] [ 9289] [depth= 1] . ( 19 sec) [ -35647.2303] [ 9288] [depth= 1] . ( 20 sec) [ -35637.5110] [ 9288] [depth= 1] . ( 20 sec) [ -35635.9827] [ 9283] [depth= 2] . ( 21 sec) [ -35632.3924] [ 9282] [depth= 1] . ( 21 sec) [ -35623.5280] [ 9283] [depth= 1] . ( 22 sec) [ -35618.2362] [ 9282] [depth= 1] . ( 22 sec) [ -35611.5147] [ 9289] [depth= 5] . ( 22 sec) [ -35589.7143] [ 9285] [depth= 2] . ( 23 sec) [ -35577.0930] [ 9281] [depth= 1] . ( 24 sec) [ -35573.3125] [ 9283] [depth= 1] . ( 24 sec) [ -35571.1524] [ 9280] [depth= 2] . ( 24 sec) [ -35568.1956] [ 9286] [depth= 1] . ( 25 sec) [ -35565.8305] [ 9290] [depth= 1] . ( 27 sec) [ -35338.2654] [Branch lengths ] . ( 35 sec) [ -35289.5052] [GTR parameters ] . ( 35 sec) [ -35281.6015] [Alpha ][ 0.446661] . ( 38 sec) [ -35281.1658] [ 9286] [depth= 1] . ( 47 sec) [ -35279.3517] [ 9283] [depth= 1] . ( 49 sec) [ -35275.5927] [ 9284] [depth= 1] . ( 50 sec) [ -35264.9091] [ 9283] [depth= 2] . ( 51 sec) [ -35263.4149] [ 9278] [depth= 1] . ( 53 sec) [ -35262.1380] [ 9282] [depth= 2] . ( 56 sec) [ -35211.6298] [Branch lengths ] . ( 61 sec) [ -35207.6802] [GTR parameters ] . ( 62 sec) [ -35207.4329] [Alpha ][ 0.455654] . ( 76 sec) [ -35197.5300] [ 9288] [depth= 1] . ( 83 sec) [ -35175.7956] [Branch lengths ] . ( 88 sec) [ -35174.5714] [GTR parameters ] . ( 88 sec) [ -35174.5073] [Alpha ][ 0.460080] . ( 97 sec) [ -35173.8353] [ 9282] [depth= 1] . ( 103 sec) [ -35173.5193] [ 9285] [depth= 1] . ( 110 sec) [ -35153.3130] [Branch lengths ] . ( 115 sec) [ -35151.9199] [GTR parameters ] . ( 116 sec) [ -35151.8521] [Alpha ][ 0.455671] . ( 137 sec) [ -35139.5436] [Branch lengths ] . ( 246 sec) [ -35138.7098] [ 9296] [depth= 2] . ( 253 sec) [ -35137.4282] [ 9292] [depth= 1] . ( 280 sec) [ -35130.8260] [Branch lengths ] . ( 286 sec) [ -35129.0070] [GTR parameters ] . ( 286 sec) [ -35128.6134] [Alpha ][ 0.445641] . ( 338 sec) [ -35127.4627] [ 9306] [depth= 2] . ( 374 sec) [ -35127.1856] [ 9319] [depth= 2] . ( 385 sec) [ -35125.4686] [ 9318] [depth= 1] . ( 392 sec) [ -35125.3332] [ 9319] [depth= 1] . ( 424 sec) [ -35117.6484] [Branch lengths ] . ( 427 sec) [ -35117.4436] [GTR parameters ] . ( 427 sec) [ -35117.3328] [Alpha ][ 0.440440] . ( 487 sec) [ -35116.9898] [ 9315] [depth= 1] . ( 509 sec) [ -35116.9440] [ 9312] [depth= 1] . ( 566 sec) [ -35113.1251] [Branch lengths ] . ( 570 sec) [ -35112.8887] [GTR parameters ] . ( 570 sec) [ -35112.8231] [Alpha ][ 0.436501] . ( 701 sec) [ -35111.0172] [Branch lengths ] . ( 701 sec) [ -35111.0172] [Topology ] . ( 705 sec) [ -35110.3825] [Topology ] . ( 708 sec) [ -35109.5275] [Topology ] . ( 711 sec) [ -35109.1213] [Topology ] . ( 714 sec) [ -35108.8541] [Topology ] . ( 717 sec) [ -35108.6663] [Topology ] . ( 719 sec) [ -35108.5320] [Topology ] . ( 723 sec) [ -35108.4352] [Topology ] . ( 727 sec) [ -35107.8179] [GTR parameters ] . ( 727 sec) [ -35107.5196] [Alpha ][ 0.428502] . ( 727 sec) [ -35107.5196] [Topology ] . ( 730 sec) [ -35107.2086] [Topology ] . ( 732 sec) [ -35107.0070] [Topology ] . ( 736 sec) [ -35106.8645] [Topology ] . ( 739 sec) [ -35106.7628] [Topology ] . ( 742 sec) [ -35106.6902] [Topology ] . ( 744 sec) [ -35106.6385] [Topology ] . ( 749 sec) [ -35106.5247] [GTR parameters ] . ( 749 sec) [ -35106.4498] [Alpha ][ 0.424580] . ( 749 sec) [ -35106.4498] [Topology ] . ( 752 sec) [ -35106.3466] [Topology ] . ( 754 sec) [ -35106.2786] [Topology ] . ( 757 sec) [ -35106.2308] [Topology ] . ( 760 sec) [ -35106.1971] [Topology ] . ( 763 sec) [ -35106.1733] [Topology ] . ( 767 sec) [ -35106.1564] [Topology ] . ( 769 sec) [ -35106.1209] [GTR parameters ] . ( 770 sec) [ -35106.0939] [Alpha ][ 0.422254] . ( 770 sec) [ -35106.0939] [Topology ] . ( 773 sec) [ -35106.0597] [Topology ] . ( 776 sec) [ -35106.0376] [Topology ] . ( 778 sec) [ -35106.0221] [Topology ] . ( 781 sec) [ -35106.0112] [Topology ] . ( 784 sec) [ -35106.0036] [Topology ] . ( 787 sec) [ -35105.9982] [Topology ] . ( 789 sec) [ -35105.9875] [GTR parameters ] . ( 790 sec) [ -35105.9783] [Alpha ][ 0.420904] . ( 790 sec) [ -35105.9783] [Topology ] . ( 793 sec) [ -35105.9671] [Topology ] . ( 795 sec) [ -35105.9598] [Topology ] . ( 798 sec) [ -35105.9548] [Topology ] . ( 800 sec) [ -35105.9513] [Topology ] . ( 803 sec) [ -35105.9488] [Topology ] . ( 806 sec) [ -35105.9471] [Topology ] . ( 807 sec) [ -35105.9446] [GTR parameters ] . ( 808 sec) [ -35105.9417] [Alpha ][ 0.420144] . ( 808 sec) [ -35105.9417] [Topology ] . ( 811 sec) [ -35105.9385] [Topology ] . ( 813 sec) [ -35105.9364] [Topology ] . ( 816 sec) [ -35105.9350] [Topology ] . ( 819 sec) [ -35105.9340] [Topology ] . ( 822 sec) [ -35105.9333] [Topology ] . ( 823 sec) [ -35105.9322] [GTR parameters ] . ( 824 sec) [ -35105.9315] [Alpha ][ 0.419723] . ( 824 sec) [ -35105.9315] [Topology ] . ( 827 sec) [ -35105.9303] [Topology ] . ( 830 sec) [ -35105.9295] [Topology ] . ( 831 sec) [ -35105.9294] [GTR parameters ] . ( 831 sec) [ -35105.9294] [Alpha ][ 0.419723] . ( 831 sec) [ -35105.9294] [Topology ] . ( 834 sec) [ -35105.9289] [Topology ] . ( 835 sec) [ -35105.9288] [GTR parameters ] . ( 835 sec) [ -35105.9288] [Alpha ][ 0.419723] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35105.928764. . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Time used 0h14m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 567.32user 0.00system 14:27.25elapsed 65%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps