.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2922_77x1101_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 . Compressing sequences... . 173 patterns found. (out of a total of 1101 sites) . 906 sites without polymorphism (82.29%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3104.2587] [Ts/ts ratio ][ 13.162306] . ( 0 sec) [ -3103.4618] [ 285] [depth= 1] . ( 0 sec) [ -3103.2908] [ 285] [depth= 1] . ( 0 sec) [ -3103.2668] [ 285] [depth= 1] . ( 1 sec) [ -3102.8024] [ 285] [depth= 1] . ( 1 sec) [ -3097.7165] [ 287] [depth= 1] . ( 3 sec) [ -3097.5921] [ 287] [depth= 1] . ( 3 sec) [ -3097.5633] [ 287] [depth= 1] . ( 3 sec) [ -3097.5373] [ 287] [depth= 1] . ( 3 sec) [ -3097.4715] [ 287] [depth= 1] . ( 3 sec) [ -3097.4516] [ 287] [depth= 1] . ( 7 sec) [ -3097.4219] [ 287] [depth= 1] . ( 7 sec) [ -3097.4119] [ 287] [depth= 1] . ( 7 sec) [ -3096.8665] [ 287] [depth= 1] . ( 7 sec) [ -3093.2500] [ 287] [depth= 3] . ( 7 sec) [ -3092.6283] [ 287] [depth= 2] . ( 7 sec) [ -3091.7142] [ 287] [depth= 4] . ( 7 sec) [ -3091.5853] [ 287] [depth= 2] . ( 7 sec) [ -3086.5790] [ 286] [depth= 1] . ( 8 sec) [ -3086.3649] [ 286] [depth= 3] . ( 8 sec) [ -3086.3443] [ 286] [depth= 2] . ( 8 sec) [ -3086.3241] [ 286] [depth= 1] . ( 8 sec) [ -3080.6124] [ 286] [depth= 4] . ( 8 sec) [ -3080.5264] [ 286] [depth= 1] . ( 8 sec) [ -3080.3754] [ 286] [depth= 1] . ( 8 sec) [ -3080.1230] [ 286] [depth= 1] . ( 8 sec) [ -3080.1124] [ 286] [depth= 1] . ( 9 sec) [ -3080.0761] [ 286] [depth= 2] . ( 10 sec) [ -3080.0656] [ 286] [depth= 1] . ( 10 sec) [ -3080.0447] [ 286] [depth= 1] . ( 10 sec) [ -3080.0190] [ 286] [depth= 1] . ( 12 sec) [ -3079.9882] [ 286] [depth= 4] . ( 12 sec) [ -3079.9598] [ 286] [depth= 1] . ( 12 sec) [ -3079.9403] [ 286] [depth= 1] . ( 12 sec) [ -3079.7888] [ 286] [depth= 2] . ( 13 sec) [ -3078.9844] [ 286] [depth= 1] . ( 14 sec) [ -3078.9464] [ 286] [depth= 1] . ( 14 sec) [ -3078.9251] [ 286] [depth= 2] . ( 15 sec) [ -3078.5407] [ 286] [depth= 2] . ( 15 sec) [ -3078.4287] [ 286] [depth= 3] . ( 15 sec) [ -3078.1687] [ 286] [depth= 1] . ( 16 sec) [ -3076.1614] [ 285] [depth= 4] . ( 17 sec) [ -3076.0022] [ 285] [depth= 1] . ( 17 sec) [ -3075.9784] [ 285] [depth= 1] . ( 19 sec) [ -3075.8649] [ 285] [depth= 1] . ( 21 sec) [ -3075.5529] [ 285] [depth= 2] . ( 21 sec) [ -3075.3136] [ 285] [depth= 2] . ( 21 sec) [ -3074.6867] [ 285] [depth= 1] . ( 21 sec) [ -3074.1412] [ 285] [depth= 1] . ( 22 sec) [ -3072.9382] [ 285] [depth= 4] . ( 22 sec) [ -3072.6675] [ 285] [depth= 2] . ( 23 sec) [ -3072.5269] [ 285] [depth= 2] . ( 23 sec) [ -3072.5109] [ 285] [depth= 2] . ( 23 sec) [ -3072.4802] [ 285] [depth= 1] . ( 29 sec) [ -3060.3036] [Branch lengths ] . ( 29 sec) [ -3060.2500] [Ts/ts ratio ][ 13.850369] . ( 37 sec) [ -3060.2384] [ 285] [depth= 1] . ( 71 sec) [ -3060.0482] [Branch lengths ] . ( 71 sec) [ -3060.0481] [Ts/ts ratio ][ 13.885973] . ( 96 sec) [ -3060.0438] [Branch lengths ] . ( 96 sec) [ -3060.0438] [Topology ] . ( 97 sec) [ -3060.0437] [Topology ] . ( 97 sec) [ -3060.0437] [Ts/ts ratio ][ 13.885973] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3060.043727. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 99 27.499432 0.979000 0.018253 100 55.344816 0.993000 0.037186 100 40.815292 0.989000 0.033778 40 0.416378 0.606000 0.001460 47 1.543455 0.355000 0.002452 45 0.643487 0.132000 0.001026 100 58.989171 0.993000 0.006946 46 -1.000000 0.000000 0.000000 75 22.591391 0.921000 0.002939 89 143.006658 1.000000 0.028902 62 35.740790 0.992000 0.005898 7 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 54 9.982117 0.827000 0.000981 25 20.146136 0.935000 0.001966 23 9.059032 0.836000 0.000984 89 25.335610 0.899000 0.001974 4 -1.000000 0.000000 0.000000 89 33.580096 0.964000 0.003993 85 4.579977 0.738000 0.000970 4 -1.000000 0.000000 0.000000 27 19.384366 0.890000 0.001979 63 11.108992 0.854000 0.000990 17 -1.000000 0.000000 0.000000 30 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 45 11.413399 0.855000 0.000991 6 -1.000000 0.000000 0.000000 63 11.372284 0.831000 0.000991 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 18 3.926705 0.743000 0.000976 83 10.986540 0.879000 0.002006 87 41.398827 0.979000 0.005334 77 13.905165 0.868000 0.002091 27 -1.000000 0.000000 0.000000 13 -1.000000 0.000000 0.000000 24 -1.000000 0.000000 0.000000 50 6.488741 0.763000 0.001049 6 -1.000000 0.000000 0.000000 41 16.265428 0.831000 0.001046 35 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 24 9.385926 0.857000 0.001046 83 21.192662 0.924000 0.002130 19 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 45 10.395621 0.847000 0.001044 9 -1.000000 0.000000 0.000000 93 58.812458 0.974000 0.004203 8 -1.000000 0.000000 0.000000 65 13.769040 0.919000 0.001034 10 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 63 11.084012 0.837000 0.001044 22 -1.000000 0.000000 0.000000 39 11.129532 0.846000 0.001044 12 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 49 10.591275 0.847000 0.000982 . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Time used 3h22m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo