.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2708_78x1107_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 . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 1107 sites) . 505 sites without polymorphism (45.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 25Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -6941.4211] [GTR parameters ] . ( 2 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 2 sec) [ -6898.9682] [ 1256] [depth= 1] . ( 3 sec) [ -6898.6922] [ 1257] [depth= 1] . ( 3 sec) [ -6862.0853] [ 1254] [depth= 1] . ( 3 sec) [ -6859.2450] [ 1256] [depth= 1] . ( 4 sec) [ -6783.6394] [ 1270] [depth= 1] . ( 4 sec) [ -6781.8295] [ 1267] [depth= 1] . ( 4 sec) [ -6779.1598] [ 1269] [depth= 1] . ( 4 sec) [ -6778.4840] [ 1271] [depth= 1] . ( 4 sec) [ -6776.5967] [ 1271] [depth= 1] . ( 4 sec) [ -6776.3316] [ 1271] [depth= 1] . ( 4 sec) [ -6776.3003] [ 1271] [depth= 1] . ( 4 sec) [ -6773.2248] [ 1271] [depth= 1] . ( 5 sec) [ -6773.1883] [ 1271] [depth= 1] . ( 5 sec) [ -6770.0884] [ 1270] [depth= 4] . ( 5 sec) [ -6751.0122] [ 1268] [depth= 2] . ( 5 sec) [ -6744.9013] [ 1268] [depth= 3] . ( 5 sec) [ -6737.5008] [ 1267] [depth= 1] . ( 5 sec) [ -6735.8779] [ 1268] [depth= 1] . ( 5 sec) [ -6735.8203] [ 1267] [depth= 1] . ( 6 sec) [ -6735.4932] [ 1267] [depth= 1] . ( 6 sec) [ -6735.1440] [ 1267] [depth= 1] . ( 6 sec) [ -6734.9653] [ 1267] [depth= 1] . ( 6 sec) [ -6734.8702] [ 1267] [depth= 3] . ( 6 sec) [ -6734.7178] [ 1267] [depth= 1] . ( 7 sec) [ -6734.0950] [ 1268] [depth= 3] . ( 7 sec) [ -6733.2735] [ 1268] [depth= 3] . ( 8 sec) [ -6713.8518] [ 1266] [depth= 2] . ( 8 sec) [ -6710.1101] [ 1266] [depth= 2] . ( 9 sec) [ -6705.9172] [ 1266] [depth= 4] . ( 9 sec) [ -6705.4473] [ 1266] [depth= 2] . ( 11 sec) [ -6705.2219] [ 1266] [depth= 1] . ( 11 sec) [ -6697.9578] [ 1265] [depth= 2] . ( 11 sec) [ -6697.4188] [ 1265] [depth= 1] . ( 12 sec) [ -6695.8394] [ 1265] [depth= 2] . ( 12 sec) [ -6695.2354] [ 1265] [depth= 1] . ( 12 sec) [ -6695.1205] [ 1262] [depth= 1] . ( 12 sec) [ -6689.8948] [ 1265] [depth= 2] . ( 12 sec) [ -6687.6406] [ 1262] [depth= 1] . ( 13 sec) [ -6687.0497] [ 1265] [depth= 2] . ( 13 sec) [ -6682.7669] [ 1266] [depth= 2] . ( 13 sec) [ -6680.4923] [ 1268] [depth= 1] . ( 13 sec) [ -6678.4931] [ 1266] [depth= 1] . ( 13 sec) [ -6670.3979] [ 1265] [depth= 1] . ( 14 sec) [ -6669.2846] [ 1264] [depth= 1] . ( 14 sec) [ -6663.6149] [ 1259] [depth= 2] . ( 14 sec) [ -6657.6884] [ 1245] [depth= 4] . ( 14 sec) [ -6657.4562] [ 1246] [depth= 1] . ( 15 sec) [ -6655.2062] [ 1246] [depth= 1] . ( 15 sec) [ -6655.1025] [ 1246] [depth= 1] . ( 15 sec) [ -6654.8410] [ 1246] [depth= 1] . ( 15 sec) [ -6653.7394] [ 1246] [depth= 2] . ( 15 sec) [ -6653.4680] [ 1246] [depth= 1] . ( 15 sec) [ -6653.4560] [ 1246] [depth= 1] . ( 17 sec) [ -6651.9113] [ 1246] [depth= 2] . ( 17 sec) [ -6646.1350] [ 1244] [depth= 1] . ( 18 sec) [ -6640.3984] [ 1245] [depth= 2] . ( 18 sec) [ -6640.3662] [ 1245] [depth= 1] . ( 18 sec) [ -6639.7977] [ 1242] [depth= 1] . ( 19 sec) [ -6638.1003] [ 1242] [depth= 2] . ( 19 sec) [ -6635.8135] [ 1241] [depth= 1] . ( 19 sec) [ -6635.3102] [ 1242] [depth= 1] . ( 20 sec) [ -6632.8656] [ 1244] [depth= 2] . ( 20 sec) [ -6628.7609] [ 1245] [depth= 1] . ( 20 sec) [ -6628.2487] [ 1245] [depth= 1] . ( 20 sec) [ -6627.4075] [ 1245] [depth= 1] . ( 20 sec) [ -6621.8047] [ 1244] [depth= 1] . ( 20 sec) [ -6615.9361] [ 1244] [depth= 1] . ( 21 sec) [ -6613.4872] [ 1244] [depth= 1] . ( 21 sec) [ -6613.4705] [ 1244] [depth= 1] . ( 22 sec) [ -6612.8261] [ 1245] [depth= 1] . ( 22 sec) [ -6608.4187] [ 1243] [depth= 1] . ( 22 sec) [ -6608.2166] [ 1243] [depth= 1] . ( 22 sec) [ -6603.3294] [ 1243] [depth= 1] . ( 22 sec) [ -6602.9630] [ 1243] [depth= 2] . ( 23 sec) [ -6602.9450] [ 1243] [depth= 2] . ( 23 sec) [ -6602.6752] [ 1243] [depth= 2] . ( 23 sec) [ -6602.6639] [ 1243] [depth= 2] . ( 24 sec) [ -6602.4765] [ 1243] [depth= 1] . ( 25 sec) [ -6602.2208] [ 1243] [depth= 5] . ( 25 sec) [ -6602.0498] [ 1243] [depth= 1] . ( 25 sec) [ -6601.9435] [ 1243] [depth= 1] . ( 25 sec) [ -6601.8804] [ 1243] [depth= 1] . ( 25 sec) [ -6601.8551] [ 1243] [depth= 3] . ( 26 sec) [ -6601.8432] [ 1243] [depth= 3] . ( 26 sec) [ -6601.5227] [ 1243] [depth= 2] . ( 26 sec) [ -6601.4694] [ 1243] [depth= 3] . ( 26 sec) [ -6601.4555] [ 1243] [depth= 1] . ( 26 sec) [ -6601.3631] [ 1243] [depth= 1] . ( 29 sec) [ -6601.3487] [ 1243] [depth= 4] . ( 30 sec) [ -6601.3128] [ 1243] [depth= 4] . ( 30 sec) [ -6601.2918] [ 1243] [depth= 3] . ( 31 sec) [ -6601.2759] [ 1243] [depth= 4] . ( 32 sec) [ -6575.1063] [Branch lengths ] . ( 35 sec) [ -6567.9357] [GTR parameters ] . ( 35 sec) [ -6563.3657] [Alpha ][ 0.408141] . ( 36 sec) [ -6563.2053] [ 1240] [depth= 1] . ( 36 sec) [ -6557.8033] [ 1263] [depth= 6] . ( 38 sec) [ -6555.4393] [ 1262] [depth= 2] . ( 38 sec) [ -6554.9281] [ 1262] [depth= 1] . ( 38 sec) [ -6554.7742] [ 1262] [depth= 1] . ( 40 sec) [ -6549.2579] [ 1267] [depth= 1] . ( 42 sec) [ -6549.0624] [ 1267] [depth= 4] . ( 45 sec) [ -6548.3324] [ 1267] [depth= 4] . ( 46 sec) [ -6547.7906] [ 1267] [depth= 1] . ( 46 sec) [ -6546.3981] [ 1262] [depth= 6] . ( 47 sec) [ -6544.4423] [ 1263] [depth= 2] . ( 49 sec) [ -6543.0174] [ 1263] [depth= 2] . ( 50 sec) [ -6540.8938] [ 1263] [depth= 1] . ( 50 sec) [ -6540.8699] [ 1263] [depth= 1] . ( 51 sec) [ -6540.3401] [ 1265] [depth= 1] . ( 61 sec) [ -6540.1386] [ 1265] [depth= 1] . ( 62 sec) [ -6540.1026] [ 1265] [depth= 1] . ( 64 sec) [ -6540.0852] [ 1266] [depth= 1] . ( 65 sec) [ -6540.0749] [ 1266] [depth= 5] . ( 73 sec) [ -6540.0588] [ 1266] [depth= 5] . ( 80 sec) [ -6533.1237] [Branch lengths ] . ( 81 sec) [ -6532.5713] [GTR parameters ] . ( 82 sec) [ -6531.6534] [Alpha ][ 0.374202] . ( 83 sec) [ -6531.4907] [ 1267] [depth= 5] . ( 84 sec) [ -6530.9669] [ 1265] [depth= 1] . ( 87 sec) [ -6530.8641] [ 1265] [depth= 5] . ( 98 sec) [ -6530.6974] [ 1264] [depth= 1] . ( 124 sec) [ -6529.1374] [Branch lengths ] . ( 126 sec) [ -6529.0886] [GTR parameters ] . ( 126 sec) [ -6528.8876] [Alpha ][ 0.359592] . ( 128 sec) [ -6528.8344] [ 1264] [depth= 1] . ( 143 sec) [ -6528.8241] [ 1264] [depth= 1] . ( 154 sec) [ -6528.7659] [ 1264] [depth= 1] . ( 154 sec) [ -6528.7502] [ 1264] [depth= 1] . ( 173 sec) [ -6528.2640] [Branch lengths ] . ( 174 sec) [ -6528.2564] [GTR parameters ] . ( 174 sec) [ -6528.2091] [Alpha ][ 0.352922] . ( 178 sec) [ -6528.1898] [ 1264] [depth= 1] . ( 179 sec) [ -6528.0575] [ 1274] [depth= 1] . ( 260 sec) [ -6527.8437] [Branch lengths ] . ( 261 sec) [ -6527.8415] [GTR parameters ] . ( 261 sec) [ -6527.8248] [Alpha ][ 0.348823] . ( 261 sec) [ -6527.8248] [Topology ] . ( 263 sec) [ -6527.7609] [Topology ] . ( 265 sec) [ -6527.7334] [Topology ] . ( 267 sec) [ -6527.7165] [Topology ] . ( 269 sec) [ -6527.7055] [Topology ] . ( 270 sec) [ -6527.6980] [Topology ] . ( 272 sec) [ -6527.6930] [Topology ] . ( 274 sec) [ -6527.6922] [GTR parameters ] . ( 274 sec) [ -6527.6855] [Alpha ][ 0.346244] . ( 274 sec) [ -6527.6855] [Topology ] . ( 276 sec) [ -6527.6787] [Topology ] . ( 278 sec) [ -6527.6756] [Topology ] . ( 279 sec) [ -6527.6736] [Topology ] . ( 281 sec) [ -6527.6722] [Topology ] . ( 283 sec) [ -6527.6713] [Topology ] . ( 284 sec) [ -6527.6711] [GTR parameters ] . ( 284 sec) [ -6527.6696] [Alpha ][ 0.345026] . ( 284 sec) [ -6527.6696] [Topology ] . ( 286 sec) [ -6527.6682] [Topology ] . ( 287 sec) [ -6527.6676] [Topology ] . ( 288 sec) [ -6527.6676] [GTR parameters ] . ( 289 sec) [ -6527.6674] [Alpha ][ 0.344575] . ( 289 sec) [ -6527.6674] [Topology ] . ( 290 sec) [ -6527.6667] [Topology ] . ( 291 sec) [ -6527.6667] [GTR parameters ] . ( 291 sec) [ -6527.6667] [Alpha ][ 0.344575] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6527.666726. . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 0h5m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 302.13user 0.00system 5:07.12elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps