.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2902_51x908_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 467 patterns found. (out of a total of 908 sites) . 480 sites without polymorphism (52.86%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7898.0075] [Ts/ts ratio ][ 3.338704] . ( 0 sec) [ -7897.9744] [ 1391] [depth= 1] . ( 1 sec) [ -7888.3847] [ 1393] [depth= 1] . ( 1 sec) [ -7877.5064] [ 1391] [depth= 1] . ( 1 sec) [ -7869.2608] [ 1389] [depth= 1] . ( 1 sec) [ -7867.0813] [ 1387] [depth= 1] . ( 1 sec) [ -7864.7291] [ 1389] [depth= 1] . ( 1 sec) [ -7864.3741] [ 1390] [depth= 1] . ( 1 sec) [ -7859.8263] [ 1389] [depth= 1] . ( 1 sec) [ -7841.5037] [ 1387] [depth= 2] . ( 2 sec) [ -7836.8040] [ 1383] [depth= 1] . ( 2 sec) [ -7822.4759] [ 1376] [depth= 3] . ( 2 sec) [ -7820.7830] [ 1379] [depth= 1] . ( 2 sec) [ -7817.7656] [ 1376] [depth= 1] . ( 2 sec) [ -7817.1064] [ 1375] [depth= 1] . ( 2 sec) [ -7813.6490] [ 1375] [depth= 1] . ( 3 sec) [ -7810.7780] [ 1375] [depth= 2] . ( 3 sec) [ -7803.0866] [ 1368] [depth= 4] . ( 3 sec) [ -7795.7326] [ 1364] [depth= 2] . ( 3 sec) [ -7795.6952] [ 1366] [depth= 1] . ( 3 sec) [ -7783.0620] [ 1371] [depth= 1] . ( 3 sec) [ -7782.7450] [ 1371] [depth= 1] . ( 4 sec) [ -7782.3467] [ 1371] [depth= 1] . ( 4 sec) [ -7781.7703] [ 1371] [depth= 1] . ( 4 sec) [ -7781.7374] [ 1371] [depth= 3] . ( 4 sec) [ -7781.6257] [ 1371] [depth= 3] . ( 4 sec) [ -7781.2854] [ 1371] [depth= 1] . ( 4 sec) [ -7775.7979] [ 1366] [depth= 1] . ( 4 sec) [ -7772.2257] [ 1368] [depth= 2] . ( 5 sec) [ -7770.4885] [ 1366] [depth= 1] . ( 5 sec) [ -7764.1973] [ 1367] [depth= 4] . ( 5 sec) [ -7755.8477] [ 1366] [depth= 2] . ( 5 sec) [ -7750.0715] [ 1364] [depth= 1] . ( 5 sec) [ -7749.3212] [ 1366] [depth= 1] . ( 5 sec) [ -7744.3925] [ 1364] [depth= 1] . ( 5 sec) [ -7744.0578] [ 1362] [depth= 3] . ( 6 sec) [ -7742.1597] [ 1364] [depth= 2] . ( 6 sec) [ -7737.3981] [ 1360] [depth= 1] . ( 6 sec) [ -7737.0358] [ 1362] [depth= 1] . ( 6 sec) [ -7736.8922] [ 1363] [depth= 1] . ( 6 sec) [ -7735.3219] [ 1362] [depth= 1] . ( 6 sec) [ -7733.9816] [ 1363] [depth= 1] . ( 6 sec) [ -7732.9181] [ 1360] [depth= 1] . ( 7 sec) [ -7732.6352] [ 1360] [depth= 1] . ( 8 sec) [ -7732.4491] [ 1358] [depth= 2] . ( 8 sec) [ -7730.7333] [ 1355] [depth= 1] . ( 10 sec) [ -7692.7286] [Branch lengths ] . ( 10 sec) [ -7691.0166] [Ts/ts ratio ][ 3.720245] . ( 11 sec) [ -7690.7415] [ 1351] [depth= 1] . ( 11 sec) [ -7690.5198] [ 1351] [depth= 1] . ( 12 sec) [ -7680.8466] [ 1348] [depth= 7] . ( 12 sec) [ -7680.7432] [ 1351] [depth= 1] . ( 12 sec) [ -7680.1581] [ 1354] [depth= 1] . ( 17 sec) [ -7680.1436] [ 1356] [depth= 1] . ( 18 sec) [ -7679.1733] [ 1355] [depth= 1] . ( 18 sec) [ -7678.5453] [ 1353] [depth= 1] . ( 18 sec) [ -7677.4016] [ 1348] [depth= 2] . ( 20 sec) [ -7677.0978] [ 1348] [depth= 1] . ( 23 sec) [ -7672.2653] [Branch lengths ] . ( 23 sec) [ -7672.2424] [Ts/ts ratio ][ 3.766817] . ( 29 sec) [ -7671.3973] [ 1348] [depth= 1] . ( 30 sec) [ -7670.8263] [ 1349] [depth= 2] . ( 35 sec) [ -7669.7686] [Branch lengths ] . ( 36 sec) [ -7669.7661] [Ts/ts ratio ][ 3.782620] . ( 41 sec) [ -7669.5857] [ 1348] [depth= 2] . ( 49 sec) [ -7669.2731] [Branch lengths ] . ( 49 sec) [ -7669.2730] [Ts/ts ratio ][ 3.786402] . ( 62 sec) [ -7669.2265] [ 1345] [depth= 1] . ( 89 sec) [ -7669.1246] [Branch lengths ] . ( 89 sec) [ -7669.1243] [Ts/ts ratio ][ 3.782219] . ( 89 sec) [ -7669.1243] [Topology ] . ( 90 sec) [ -7669.1224] [Topology ] . ( 91 sec) [ -7669.1221] [Topology ] . ( 91 sec) [ -7669.1221] [Ts/ts ratio ][ 3.782219] . ( 91 sec) [ -7669.1221] [Topology ] . ( 92 sec) [ -7669.1220] [Topology ] . ( 92 sec) [ -7669.1220] [Ts/ts ratio ][ 3.782219] . Checking for NNIs, optimizing five branches... . ( 100 sec) [ -7669.0920] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7669.092011. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 68.566068 0.999000 0.042724 54 10.187606 0.768000 0.030084 100 187.787568 1.000000 0.114560 50 10.879701 0.906000 0.033056 100 192.884432 1.000000 0.157962 8 0.060055 0.000000 0.003421 16 17.356315 0.934000 0.020521 53 9.351311 0.884000 0.016494 100 50.028126 0.990000 0.034201 100 46.923807 0.994000 0.059009 8 7.146118 0.875000 0.017004 8 1.022784 0.316000 0.007958 10 1.688253 0.669000 0.005534 96 46.750603 0.993000 0.045002 60 0.749045 0.144000 0.009189 63 11.354304 0.882000 0.014704 17 7.177043 0.650000 0.012673 100 89.479990 1.000000 0.053271 97 25.085216 0.967000 0.020436 46 11.113737 0.851000 0.013101 62 4.215799 0.638000 0.010870 53 7.995179 0.738000 0.026314 93 26.738750 0.955000 0.023659 42 4.171678 0.807000 0.022381 100 150.226877 1.000000 0.154830 33 0.787645 0.327000 0.009300 31 -1.000000 0.000000 0.000003 21 5.116170 0.674000 0.007437 19 18.220562 0.944000 0.019996 13 9.988665 0.870000 0.009179 5 0.938746 0.241000 0.007672 88 32.442796 0.965000 0.027295 48 3.658356 0.377000 0.014890 100 152.661427 1.000000 0.138890 100 13.125119 0.905000 0.017816 44 1.333302 0.727000 0.002200 14 -1.000000 0.000000 0.000000 20 -1.000000 0.000000 0.000000 9 4.297487 0.489000 0.006496 22 3.302712 0.794000 0.006860 98 83.483963 0.999000 0.039568 59 0.160384 0.000000 0.001515 68 12.765699 0.854000 0.003011 71 6.358044 0.779000 0.001517 21 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 30 2.420145 0.755000 0.006090 96 23.960906 0.956000 0.021259 . Printing the most likely tree in file 'nucleic_M2902_51x908_2006.phy_phyml_tree.txt'... . Time used 2h26m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo