.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1376_36x484_2003.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : LG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : no . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 392 patterns found. (out of a total of 484 sites) . 132 sites without polymorphism (27.27%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 34Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11531.3108] [ 1985] [depth= 2] . ( 2 sec) [ -11521.4026] [ 1984] [depth= 1] . ( 2 sec) [ -11519.9384] [ 1985] [depth= 1] . ( 5 sec) [ -11518.3521] [ 1982] [depth= 1] . ( 7 sec) [ -11508.8198] [ 1988] [depth= 2] . ( 7 sec) [ -11508.0875] [ 1983] [depth= 2] . ( 8 sec) [ -11507.3326] [ 1984] [depth= 2] . ( 9 sec) [ -11501.2244] [ 1978] [depth= 2] . ( 11 sec) [ -11501.0600] [ 1977] [depth= 1] . ( 12 sec) [ -11500.1570] [ 1980] [depth= 1] . ( 13 sec) [ -11499.9746] [ 1982] [depth= 1] . ( 15 sec) [ -11499.3723] [ 1980] [depth= 1] . ( 28 sec) [ -11497.2479] [ 1982] [depth= 1] . ( 28 sec) [ -11495.8758] [ 1980] [depth= 1] . ( 33 sec) [ -11495.1809] [ 1982] [depth= 1] . ( 35 sec) [ -11490.1711] [ 1981] [depth= 1] . ( 36 sec) [ -11486.7976] [ 1982] [depth= 1] . ( 39 sec) [ -11484.8621] [ 1986] [depth= 1] . ( 39 sec) [ -11484.2646] [ 1984] [depth= 1] . ( 40 sec) [ -11482.8325] [ 1980] [depth= 1] . ( 41 sec) [ -11481.5576] [ 1979] [depth= 1] . ( 42 sec) [ -11480.1022] [ 1980] [depth= 1] . ( 47 sec) [ -11479.6127] [ 1981] [depth= 1] . ( 52 sec) [ -11479.5337] [ 1980] [depth= 1] . ( 57 sec) [ -11447.0713] [Branch lengths ] . ( 59 sec) [ -11446.4925] [ 1979] [depth= 1] . ( 66 sec) [ -11446.3093] [ 1977] [depth= 2] . ( 66 sec) [ -11445.4012] [ 1976] [depth= 1] . ( 69 sec) [ -11443.4906] [ 1979] [depth= 1] . ( 104 sec) [ -11442.7525] [ 1978] [depth= 1] . ( 122 sec) [ -11436.9505] [Branch lengths ] . ( 154 sec) [ -11436.8963] [ 1978] [depth= 1] . ( 163 sec) [ -11436.6815] [ 1978] [depth= 1] . ( 189 sec) [ -11435.8730] [Branch lengths ] . ( 258 sec) [ -11435.8174] [Branch lengths ] . ( 259 sec) [ -11435.8174] [Topology ] . ( 262 sec) [ -11435.8124] [Topology ] . ( 265 sec) [ -11435.8107] [Topology ] . ( 268 sec) [ -11435.8098] [Topology ] . ( 268 sec) [ -11435.8098] [Topology ] . ( 272 sec) [ -11435.8093] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11435.809316. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 62.577557 0.995000 0.153338 39 2.961988 0.297000 0.058328 25 4.708127 0.829000 0.020892 8 1.843116 0.405000 0.015098 27 8.911752 0.812000 0.029287 100 400.061543 1.000000 0.523526 99 39.773785 0.985000 0.130785 97 42.579965 0.990000 0.096862 50 8.853952 0.825000 0.018871 38 4.754551 0.309000 0.022206 38 2.526728 0.742000 0.009160 57 6.509858 0.637000 0.029632 95 43.581855 0.983000 0.110221 98 51.965966 0.994000 0.153842 78 13.299068 0.853000 0.023772 63 10.918581 0.638000 0.033355 5 22.061524 0.929000 0.026522 84 33.968259 0.966000 0.035310 74 18.807578 0.905000 0.024284 16 1.041308 0.257000 0.005179 84 36.437402 0.986000 0.049893 30 9.434844 0.863000 0.010746 49 16.914943 0.868000 0.013504 17 6.382088 0.774000 0.012680 31 4.606360 0.408000 0.015756 30 4.104552 0.486000 0.014983 97 38.311387 0.979000 0.029422 19 1.051304 0.113000 0.011579 59 21.303916 0.926000 0.015002 90 14.801601 0.897000 0.016446 100 66.922887 0.996000 0.038498 13 8.394797 0.857000 0.017016 52 9.414435 0.886000 0.030548 . Printing the most likely tree in file 'proteic_M1376_36x484_2003.phy_phyml_tree.txt'... . Time used 6h28m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo