.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1992_46x68_2004.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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 . Compressing sequences... . 68 patterns found. (out of a total of 68 sites) . 1 sites without polymorphism (1.47%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -3015.2739] [Alpha ][ 1.996970] . ( 1 sec) [ -3015.2739] [Topology ] . ( 2 sec) [ -2947.5324] [Topology ] . ( 3 sec) [ -2935.3074] [Topology ] . ( 4 sec) [ -2930.3388] [Topology ] . ( 5 sec) [ -2927.4368] [Topology ] . ( 6 sec) [ -2926.9560] [Topology ] . ( 7 sec) [ -2926.8177] [Topology ] . ( 8 sec) [ -2926.7584] [Topology ] . ( 9 sec) [ -2926.7265] [Topology ] . ( 10 sec) [ -2926.7072] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -2926.5115] [Topology ] . ( 17 sec) [ -2922.8546] [Alpha ][ 3.815477] . ( 17 sec) [ -2922.8546] [Topology ] . ( 18 sec) [ -2921.6808] [Topology ] . ( 19 sec) [ -2921.4624] [Topology ] . ( 20 sec) [ -2921.4165] [Topology ] . ( 21 sec) [ -2921.4036] [Topology ] . ( 22 sec) [ -2921.3998] [Topology ] . ( 23 sec) [ -2921.3987] [Topology ] . ( 24 sec) [ -2921.3983] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -2921.3961] [Alpha ][ 3.883619] . ( 31 sec) [ -2921.3961] [Topology ] . ( 32 sec) [ -2921.3960] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -2921.3960] [Alpha ][ 3.883619] . ( 39 sec) [ -2921.3960] [Topology ] . ( 40 sec) [ -2921.3959] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -3015.2739] [Alpha ][ 1.996970] . ( 55 sec) [ -3009.8145] [ 596] [depth= 1] . ( 55 sec) [ -3008.6553] [ 596] [depth= 1] . ( 56 sec) [ -3008.0825] [ 596] [depth= 1] . ( 56 sec) [ -3007.9894] [ 596] [depth= 1] . ( 56 sec) [ -3007.8324] [ 596] [depth= 1] . ( 57 sec) [ -2984.1112] [ 596] [depth= 4] . ( 57 sec) [ -2970.8096] [ 596] [depth= 3] . ( 58 sec) [ -2969.9180] [ 594] [depth= 3] . ( 58 sec) [ -2968.9224] [ 593] [depth= 4] . ( 58 sec) [ -2968.5292] [ 594] [depth= 2] . ( 58 sec) [ -2960.2240] [ 594] [depth= 1] . ( 60 sec) [ -2958.9926] [ 597] [depth= 2] . ( 61 sec) [ -2957.9119] [ 597] [depth= 1] . ( 61 sec) [ -2956.0693] [ 593] [depth= 1] . ( 62 sec) [ -2955.2325] [ 597] [depth= 1] . ( 62 sec) [ -2954.5183] [ 597] [depth= 1] . ( 62 sec) [ -2954.1297] [ 597] [depth= 1] . ( 62 sec) [ -2954.0281] [ 597] [depth= 1] . ( 63 sec) [ -2953.9961] [ 597] [depth= 1] . ( 65 sec) [ -2953.9681] [ 593] [depth= 1] . ( 65 sec) [ -2953.6735] [ 595] [depth= 2] . ( 65 sec) [ -2953.3501] [ 595] [depth= 1] . ( 65 sec) [ -2952.7980] [ 595] [depth= 1] . ( 69 sec) [ -2951.9097] [ 597] [depth= 2] . ( 70 sec) [ -2950.5572] [ 597] [depth= 1] . ( 71 sec) [ -2948.1402] [ 596] [depth= 1] . ( 72 sec) [ -2947.0059] [ 595] [depth= 3] . ( 74 sec) [ -2946.6394] [ 593] [depth= 2] . ( 74 sec) [ -2945.1957] [ 595] [depth= 1] . ( 74 sec) [ -2943.6144] [ 595] [depth= 1] . ( 75 sec) [ -2943.2339] [ 596] [depth= 1] . ( 77 sec) [ -2942.6632] [ 597] [depth= 2] . ( 77 sec) [ -2942.6429] [ 597] [depth= 1] . ( 77 sec) [ -2942.5838] [ 597] [depth= 1] . ( 77 sec) [ -2942.4906] [ 597] [depth= 1] . ( 78 sec) [ -2942.4054] [ 597] [depth= 1] . ( 79 sec) [ -2942.3926] [ 598] [depth= 1] . ( 79 sec) [ -2941.8188] [ 599] [depth= 1] . ( 79 sec) [ -2937.6111] [ 599] [depth= 1] . ( 83 sec) [ -2937.3528] [ 597] [depth= 1] . ( 84 sec) [ -2935.4339] [ 597] [depth= 1] . ( 85 sec) [ -2926.7740] [Branch lengths ] . ( 86 sec) [ -2923.7857] [Alpha ][ 3.533893] . ( 91 sec) [ -2923.0855] [ 597] [depth= 1] . ( 101 sec) [ -2922.9826] [ 597] [depth= 3] . ( 101 sec) [ -2922.9582] [ 592] [depth= 13] . ( 126 sec) [ -2922.3548] [Branch lengths ] . ( 126 sec) [ -2922.3434] [Alpha ][ 3.670174] . ( 136 sec) [ -2922.3323] [ 594] [depth= 1] . ( 166 sec) [ -2922.2811] [Branch lengths ] . ( 166 sec) [ -2922.2811] [Alpha ][ 3.675766] . ( 166 sec) [ -2922.2811] [Topology ] . ( 167 sec) [ -2922.2760] [Topology ] . ( 168 sec) [ -2922.2745] [Topology ] . ( 169 sec) [ -2922.2739] [Topology ] . ( 169 sec) [ -2922.2739] [Alpha ][ 3.675766] . ( 169 sec) [ -2922.2739] [Topology ] . ( 170 sec) [ -2922.2737] [Topology ] . ( 170 sec) [ -2922.2737] [Alpha ][ 3.675766] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2921.395934 . Log likelihood obtained after SPR moves : -2922.273687 . Log likelihood of the current tree: -2921.395934. . Printing the most likely tree in file 'proteic_M1992_46x68_2004.phy_phyml_tree.txt'... . Time used 0h2m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 172.54user 0.00system 2:56.91elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps