.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 6 sec) [ -12703.7048] [GTR parameters ] . ( 6 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 6 sec) [ -12506.3721] [Topology ] . ( 8 sec) [ -12215.6080] [Topology ] . ( 10 sec) [ -12152.0977] [Topology ] . ( 13 sec) [ -12139.1352] [Topology ] . ( 15 sec) [ -12126.7129] [Topology ] . ( 17 sec) [ -12130.9985] [Topology ] . Moving backward . ( 17 sec) [ -12121.4353] [Topology ] . ( 19 sec) [ -12122.7329] [Topology ] . Moving backward . ( 19 sec) [ -12118.4950] [Topology ] . ( 21 sec) [ -12116.6881] [Topology ] . ( 25 sec) [ -12094.3714] [GTR parameters ] . ( 25 sec) [ -12054.0715] [Alpha ][ 0.324674] . ( 25 sec) [ -12054.0715] [Topology ] . ( 27 sec) [ -12046.5550] [Topology ] . ( 29 sec) [ -12049.9254] [Topology ] . Moving backward . ( 29 sec) [ -12041.0508] [Topology ] . ( 31 sec) [ -12039.5299] [Topology ] . ( 33 sec) [ -12040.3282] [Topology ] . Moving backward . ( 33 sec) [ -12035.7717] [Topology ] . ( 35 sec) [ -12034.7699] [Topology ] . ( 37 sec) [ -12034.6451] [Topology ] . ( 39 sec) [ -12034.0025] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -12034.0255] [Topology ] . ( 57 sec) [ -12030.5971] [GTR parameters ] . ( 57 sec) [ -12029.8024] [Alpha ][ 0.306568] . ( 57 sec) [ -12029.8024] [Topology ] . ( 59 sec) [ -12029.0738] [Topology ] . ( 61 sec) [ -12029.0786] [Topology ] . Moving backward . ( 61 sec) [ -12028.8782] [Topology ] . ( 63 sec) [ -12028.8209] [Topology ] . ( 65 sec) [ -12029.0361] [Topology ] . Moving backward . ( 65 sec) [ -12028.6691] [Topology ] . ( 67 sec) [ -12028.6702] [Topology ] . Moving backward . ( 67 sec) [ -12028.5546] [Topology ] . ( 69 sec) [ -12028.4954] [Topology ] . Checking for NNIs, optimizing five branches... . ( 84 sec) [ -12028.4944] [Topology ] . ( 86 sec) [ -12028.2370] [GTR parameters ] . ( 86 sec) [ -12028.1961] [Alpha ][ 0.302803] . ( 86 sec) [ -12028.1961] [Topology ] . ( 88 sec) [ -12028.0997] [Topology ] . ( 90 sec) [ -12028.1125] [Topology ] . Moving backward . ( 90 sec) [ -12028.0660] [Topology ] . ( 92 sec) [ -12028.1322] [Topology ] . Moving backward . ( 92 sec) [ -12028.0427] [Topology ] . ( 94 sec) [ -12028.0742] [Topology ] . Moving backward . ( 94 sec) [ -12028.0259] [Topology ] . ( 96 sec) [ -12028.1259] [Topology ] . Moving backward . ( 96 sec) [ -12028.0120] [Topology ] . Checking for NNIs, optimizing five branches... . ( 112 sec) [ -12028.0710] [Topology ] . ( 114 sec) [ -12028.0401] [GTR parameters ] . ( 114 sec) [ -12028.0365] [Alpha ][ 0.301588] . ( 114 sec) [ -12028.0365] [Topology ] . ( 116 sec) [ -12028.0205] [Topology ] . ( 118 sec) [ -12028.4083] [Topology ] . Moving backward . ( 118 sec) [ -12027.9769] [Topology ] . ( 120 sec) [ -12028.0037] [Topology ] . Moving backward . ( 120 sec) [ -12027.8763] [Topology ] . ( 122 sec) [ -12027.8675] [Topology ] . ( 124 sec) [ -12027.9072] [Topology ] . Moving backward . ( 124 sec) [ -12027.8644] [Topology ] . ( 126 sec) [ -12027.9897] [Topology ] . Checking for NNIs, optimizing five branches... . ( 141 sec) [ -12027.8083] [Topology ] . ( 142 sec) [ -12027.8011] [GTR parameters ] . ( 142 sec) [ -12027.8005] [Alpha ][ 0.301093] . ( 142 sec) [ -12027.8005] [Topology ] . ( 144 sec) [ -12027.7950] [Topology ] . ( 146 sec) [ -12027.8067] [Topology ] . Moving backward . ( 146 sec) [ -12027.7946] [Topology ] . Checking for NNIs, optimizing five branches... . ( 160 sec) [ -12027.7925] [Topology ] . ( 161 sec) [ -12027.7921] [GTR parameters ] . ( 161 sec) [ -12027.7921] [Alpha ][ 0.301093] . ( 161 sec) [ -12027.7921] [Topology ] . ( 163 sec) [ -12027.7894] [Topology ] . ( 165 sec) [ -12027.7894] [Topology ] . Checking for NNIs, optimizing five branches... . ( 180 sec) [ -12027.7807] [Topology ] . ( 180 sec) [ -12027.7806] [GTR parameters ] . ( 180 sec) [ -12027.7806] [Alpha ][ 0.301093] . ( 180 sec) [ -12027.7806] [Topology ] . ( 182 sec) [ -12027.7797] [Topology ] . Checking for NNIs, optimizing five branches... . ( 197 sec) [ -12027.7796] [Topology ] . ( 197 sec) [ -12027.7796] [GTR parameters ] . ( 197 sec) [ -12027.7796] [Alpha ][ 0.301093] . ( 197 sec) [ -12027.7796] [Topology ] . ( 199 sec) [ -12027.7790] [Topology ] . Checking for NNIs, optimizing five branches... . ( 213 sec) [ -12027.7789] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 233 sec) [ -12703.7048] [GTR parameters ] . ( 233 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 233 sec) [ -12504.9636] [ 2715] [depth= 1] . ( 233 sec) [ -12504.7654] [ 2715] [depth= 1] . ( 234 sec) [ -12497.1136] [ 2715] [depth= 1] . ( 234 sec) [ -12493.5302] [ 2715] [depth= 1] . ( 234 sec) [ -12491.3616] [ 2715] [depth= 1] . ( 234 sec) [ -12483.4602] [ 2713] [depth= 2] . ( 234 sec) [ -12482.5118] [ 2713] [depth= 1] . ( 234 sec) [ -12482.4575] [ 2713] [depth= 1] . ( 234 sec) [ -12470.4830] [ 2713] [depth= 1] . ( 235 sec) [ -12466.0686] [ 2713] [depth= 1] . ( 235 sec) [ -12465.9179] [ 2713] [depth= 1] . ( 235 sec) [ -12449.2031] [ 2705] [depth= 1] . ( 235 sec) [ -12449.1587] [ 2705] [depth= 1] . ( 235 sec) [ -12437.2290] [ 2704] [depth= 1] . ( 235 sec) [ -12432.0204] [ 2705] [depth= 1] . ( 236 sec) [ -12431.2264] [ 2705] [depth= 1] . ( 236 sec) [ -12431.1803] [ 2705] [depth= 1] . ( 236 sec) [ -12414.3902] [ 2705] [depth= 1] . ( 237 sec) [ -12397.8831] [ 2704] [depth= 1] . ( 237 sec) [ -12388.4419] [ 2704] [depth= 1] . ( 237 sec) [ -12357.7085] [ 2703] [depth= 4] . ( 237 sec) [ -12340.0539] [ 2692] [depth= 4] . ( 237 sec) [ -12337.3933] [ 2693] [depth= 1] . ( 237 sec) [ -12290.3349] [ 2697] [depth= 1] . ( 238 sec) [ -12276.7111] [ 2700] [depth= 1] . ( 238 sec) [ -12275.6885] [ 2702] [depth= 2] . ( 238 sec) [ -12275.1313] [ 2706] [depth= 1] . ( 238 sec) [ -12274.3385] [ 2703] [depth= 1] . ( 238 sec) [ -12272.9383] [ 2701] [depth= 1] . ( 238 sec) [ -12266.5292] [ 2692] [depth= 2] . ( 239 sec) [ -12256.4860] [ 2690] [depth= 2] . ( 239 sec) [ -12252.4458] [ 2688] [depth= 1] . ( 239 sec) [ -12248.8610] [ 2682] [depth= 2] . ( 239 sec) [ -12248.1344] [ 2687] [depth= 2] . ( 240 sec) [ -12246.6557] [ 2687] [depth= 1] . ( 241 sec) [ -12246.3006] [ 2689] [depth= 1] . ( 241 sec) [ -12217.8872] [ 2684] [depth= 1] . ( 242 sec) [ -12209.5068] [ 2684] [depth= 1] . ( 242 sec) [ -12207.6577] [ 2684] [depth= 1] . ( 242 sec) [ -12207.6325] [ 2684] [depth= 2] . ( 242 sec) [ -12207.0453] [ 2684] [depth= 1] . ( 242 sec) [ -12206.9176] [ 2684] [depth= 1] . ( 242 sec) [ -12206.6771] [ 2684] [depth= 1] . ( 248 sec) [ -12205.6860] [ 2684] [depth= 1] . ( 248 sec) [ -12203.4087] [ 2684] [depth= 1] . ( 248 sec) [ -12203.3920] [ 2684] [depth= 6] . ( 248 sec) [ -12203.3687] [ 2684] [depth= 7] . ( 249 sec) [ -12198.4249] [ 2685] [depth= 9] . ( 249 sec) [ -12194.4738] [ 2684] [depth= 9] . ( 250 sec) [ -12192.8649] [ 2683] [depth= 3] . ( 250 sec) [ -12191.5426] [ 2683] [depth= 3] . ( 251 sec) [ -12191.0843] [ 2683] [depth= 1] . ( 251 sec) [ -12190.8974] [ 2683] [depth= 1] . ( 251 sec) [ -12190.8719] [ 2683] [depth= 2] . ( 251 sec) [ -12190.8488] [ 2683] [depth= 6] . ( 251 sec) [ -12190.8090] [ 2683] [depth= 6] . ( 252 sec) [ -12190.7862] [ 2683] [depth= 3] . ( 262 sec) [ -12121.2317] [Branch lengths ] . ( 264 sec) [ -12102.7305] [GTR parameters ] . ( 264 sec) [ -12064.9048] [Alpha ][ 0.326790] . ( 266 sec) [ -12064.8902] [ 2683] [depth= 1] . ( 267 sec) [ -12064.7775] [ 2680] [depth= 2] . ( 267 sec) [ -12064.2603] [ 2684] [depth= 2] . ( 267 sec) [ -12064.2338] [ 2684] [depth= 1] . ( 267 sec) [ -12060.1695] [ 2683] [depth= 1] . ( 268 sec) [ -12057.9052] [ 2680] [depth= 2] . ( 269 sec) [ -12052.4725] [ 2683] [depth= 3] . ( 270 sec) [ -12050.5920] [ 2678] [depth= 1] . ( 280 sec) [ -12050.5800] [ 2678] [depth= 1] . ( 281 sec) [ -12050.5672] [ 2678] [depth= 1] . ( 296 sec) [ -12040.1040] [Branch lengths ] . ( 299 sec) [ -12035.8716] [GTR parameters ] . ( 299 sec) [ -12035.2488] [Alpha ][ 0.310434] . ( 302 sec) [ -12035.1353] [ 2678] [depth= 1] . ( 304 sec) [ -12035.0962] [ 2678] [depth= 1] . ( 305 sec) [ -12034.2176] [ 2683] [depth= 2] . ( 317 sec) [ -12034.2061] [ 2683] [depth= 9] . ( 330 sec) [ -12030.7991] [Branch lengths ] . ( 334 sec) [ -12030.3420] [GTR parameters ] . ( 334 sec) [ -12030.3032] [Alpha ][ 0.306697] . ( 336 sec) [ -12030.2795] [ 2683] [depth= 1] . ( 366 sec) [ -12029.0319] [Branch lengths ] . ( 368 sec) [ -12028.9324] [GTR parameters ] . ( 368 sec) [ -12028.9229] [Alpha ][ 0.304719] . ( 400 sec) [ -12028.3656] [Branch lengths ] . ( 476 sec) [ -12027.5935] [Branch lengths ] . ( 476 sec) [ -12027.5935] [Topology ] . ( 478 sec) [ -12026.0225] [Topology ] . ( 479 sec) [ -12023.9745] [Topology ] . ( 481 sec) [ -12023.2568] [Topology ] . ( 483 sec) [ -12023.0084] [Topology ] . ( 485 sec) [ -12022.9239] [Topology ] . ( 486 sec) [ -12022.8906] [Topology ] . ( 487 sec) [ -12022.7514] [GTR parameters ] . ( 488 sec) [ -12022.7392] [Alpha ][ 0.302503] . ( 488 sec) [ -12022.7392] [Topology ] . ( 490 sec) [ -12022.7114] [Topology ] . ( 491 sec) [ -12022.7006] [Topology ] . ( 493 sec) [ -12022.6955] [Topology ] . ( 495 sec) [ -12022.6929] [Topology ] . ( 497 sec) [ -12022.6916] [Topology ] . ( 498 sec) [ -12022.6909] [Topology ] . ( 500 sec) [ -12022.6850] [GTR parameters ] . ( 500 sec) [ -12022.6842] [Alpha ][ 0.301899] . ( 500 sec) [ -12022.6842] [Topology ] . ( 502 sec) [ -12022.6823] [Topology ] . ( 504 sec) [ -12022.6814] [Topology ] . ( 504 sec) [ -12022.6810] [GTR parameters ] . ( 505 sec) [ -12022.6810] [Alpha ][ 0.301899] . ( 505 sec) [ -12022.6810] [Topology ] . ( 506 sec) [ -12022.6803] [Topology ] . ( 507 sec) [ -12022.6802] [GTR parameters ] . ( 507 sec) [ -12022.6802] [Alpha ][ 0.301899] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12027.778921 . Log likelihood obtained after SPR moves : -12022.680231 . Log likelihood of the current tree: -12022.680231. . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 0h8m42s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 520.02user 0.00system 8:42.49elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps