.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1384_11x391_2003.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 : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 195 patterns found. (out of a total of 391 sites) . 216 sites without polymorphism (55.24%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3274.7054] [Alpha ][ 0.500960] . ( 1 sec) [ -3175.6010] [ 381] [depth= 4] . ( 1 sec) [ -3157.2425] [ 380] [depth= 1] . ( 1 sec) [ -3121.2942] [ 380] [depth= 2] . ( 1 sec) [ -3084.2788] [ 365] [depth= 1] . ( 1 sec) [ -3056.7178] [ 361] [depth= 4] . ( 1 sec) [ -3041.2207] [ 360] [depth= 1] . ( 1 sec) [ -3032.9660] [ 357] [depth= 2] . ( 2 sec) [ -3031.8070] [ 358] [depth= 1] . ( 2 sec) [ -3031.5860] [ 361] [depth= 1] . ( 2 sec) [ -3014.7161] [ 358] [depth= 1] . ( 2 sec) [ -3005.1480] [ 357] [depth= 1] . ( 2 sec) [ -2974.0367] [ 358] [depth= 4] . ( 2 sec) [ -2952.2003] [ 349] [depth= 1] . ( 3 sec) [ -2946.7121] [ 349] [depth= 2] . ( 3 sec) [ -2942.2574] [ 349] [depth= 1] . ( 4 sec) [ -2935.2934] [ 344] [depth= 2] . ( 4 sec) [ -2926.9657] [ 345] [depth= 5] . ( 4 sec) [ -2895.2339] [Branch lengths ] . ( 4 sec) [ -2894.7136] [Alpha ][ 0.588334] . ( 4 sec) [ -2890.2150] [ 341] [depth= 1] . ( 8 sec) [ -2884.8757] [ 340] [depth= 5] . ( 8 sec) [ -2884.7320] [ 340] [depth= 1] . ( 10 sec) [ -2884.6775] [ 340] [depth= 1] . ( 11 sec) [ -2884.6081] [ 340] [depth= 1] . ( 13 sec) [ -2882.8910] [Branch lengths ] . ( 13 sec) [ -2882.8827] [Alpha ][ 0.600777] . ( 25 sec) [ -2882.7927] [Branch lengths ] . ( 25 sec) [ -2882.7927] [Topology ] . ( 25 sec) [ -2882.7921] [Topology ] . ( 25 sec) [ -2882.7920] [Alpha ][ 0.601695] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2882.792022. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3674.7374] [Alpha ][ 0.500960] . ( 0 sec) [ -3366.0709] [ 392] [depth= 3] . ( 0 sec) [ -3148.7696] [ 389] [depth= 1] . ( 0 sec) [ -3122.0858] [ 387] [depth= 2] . ( 0 sec) [ -3111.8136] [ 387] [depth= 1] . ( 0 sec) [ -3109.9438] [ 387] [depth= 1] . ( 1 sec) [ -3044.0155] [ 384] [depth= 5] . ( 1 sec) [ -3041.3929] [ 380] [depth= 4] . ( 1 sec) [ -3033.6667] [ 371] [depth= 1] . ( 1 sec) [ -2972.6145] [ 366] [depth= 5] . ( 1 sec) [ -2970.9756] [ 368] [depth= 1] . ( 1 sec) [ -2968.7273] [ 371] [depth= 1] . ( 1 sec) [ -2964.7758] [ 369] [depth= 2] . ( 1 sec) [ -2920.5939] [ 349] [depth= 1] . ( 1 sec) [ -2920.3736] [ 349] [depth= 1] . ( 2 sec) [ -2913.4758] [ 347] [depth= 1] . ( 2 sec) [ -2912.6613] [ 343] [depth= 1] . ( 2 sec) [ -2911.5658] [ 343] [depth= 1] . ( 2 sec) [ -2907.5293] [ 342] [depth= 2] . ( 3 sec) [ -2904.6721] [ 342] [depth= 2] . ( 3 sec) [ -2898.4718] [ 342] [depth= 1] . ( 4 sec) [ -2889.3890] [Branch lengths ] . ( 4 sec) [ -2888.7867] [Alpha ][ 0.595755] . ( 7 sec) [ -2883.7645] [ 340] [depth= 6] . ( 8 sec) [ -2883.6942] [ 340] [depth= 1] . ( 8 sec) [ -2883.6495] [ 340] [depth= 1] . ( 13 sec) [ -2882.8365] [Branch lengths ] . ( 13 sec) [ -2882.8326] [Alpha ][ 0.604773] . ( 19 sec) [ -2882.8219] [ 340] [depth= 1] . ( 24 sec) [ -2882.7927] [Branch lengths ] . ( 24 sec) [ -2882.7924] [Alpha ][ 0.601932] . ( 24 sec) [ -2882.7924] [Topology ] . ( 24 sec) [ -2882.7919] [Topology ] . ( 24 sec) [ -2882.7919] [Alpha ][ 0.601932] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2882.791910. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3690.3799] [Alpha ][ 0.500960] . ( 0 sec) [ -3593.9901] [ 389] [depth= 1] . ( 0 sec) [ -3502.9250] [ 383] [depth= 2] . ( 0 sec) [ -3498.0382] [ 385] [depth= 1] . ( 0 sec) [ -3467.4564] [ 388] [depth= 1] . ( 1 sec) [ -3411.3054] [ 383] [depth= 3] . ( 1 sec) [ -3408.9350] [ 382] [depth= 1] . ( 1 sec) [ -3302.7780] [ 376] [depth= 2] . ( 1 sec) [ -3230.1217] [ 374] [depth= 2] . ( 1 sec) [ -2996.2980] [ 374] [depth= 1] . ( 1 sec) [ -2991.6998] [ 370] [depth= 1] . ( 1 sec) [ -2968.3507] [ 369] [depth= 2] . ( 1 sec) [ -2951.7729] [ 352] [depth= 2] . ( 1 sec) [ -2914.7302] [ 342] [depth= 1] . ( 1 sec) [ -2900.6232] [ 343] [depth= 1] . ( 3 sec) [ -2898.5284] [ 343] [depth= 1] . ( 3 sec) [ -2894.7568] [ 342] [depth= 1] . ( 3 sec) [ -2892.1578] [ 340] [depth= 2] . ( 3 sec) [ -2892.0645] [ 340] [depth= 1] . ( 3 sec) [ -2890.4511] [ 340] [depth= 1] . ( 4 sec) [ -2888.5451] [ 340] [depth= 1] . ( 4 sec) [ -2883.5855] [Branch lengths ] . ( 4 sec) [ -2882.9378] [Alpha ][ 0.601341] . ( 7 sec) [ -2882.9278] [ 340] [depth= 1] . ( 14 sec) [ -2882.7953] [Branch lengths ] . ( 14 sec) [ -2882.7953] [Alpha ][ 0.602255] . ( 14 sec) [ -2882.7953] [Topology ] . ( 15 sec) [ -2882.7924] [Topology ] . ( 15 sec) [ -2882.7919] [Topology ] . ( 15 sec) [ -2882.7919] [Alpha ][ 0.601653] . ( 15 sec) [ -2882.7919] [Topology ] . ( 16 sec) [ -2882.7918] [Topology ] . ( 16 sec) [ -2882.7918] [Alpha ][ 0.601653] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2882.791823. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3421.7780] [Alpha ][ 0.500960] . ( 1 sec) [ -3414.1861] [ 361] [depth= 2] . ( 1 sec) [ -3380.8483] [ 360] [depth= 3] . ( 1 sec) [ -3311.5587] [ 359] [depth= 1] . ( 1 sec) [ -3233.6165] [ 355] [depth= 2] . ( 1 sec) [ -3227.0836] [ 356] [depth= 1] . ( 1 sec) [ -2954.9236] [ 358] [depth= 1] . ( 1 sec) [ -2951.0314] [ 360] [depth= 2] . ( 1 sec) [ -2943.7123] [ 360] [depth= 2] . ( 1 sec) [ -2943.6605] [ 360] [depth= 2] . ( 1 sec) [ -2925.8867] [ 350] [depth= 3] . ( 2 sec) [ -2923.0745] [ 348] [depth= 2] . ( 2 sec) [ -2916.0821] [ 341] [depth= 1] . ( 2 sec) [ -2902.6998] [ 341] [depth= 1] . ( 2 sec) [ -2900.9502] [ 341] [depth= 1] . ( 3 sec) [ -2900.8157] [ 341] [depth= 1] . ( 6 sec) [ -2890.2269] [Branch lengths ] . ( 6 sec) [ -2889.6642] [Alpha ][ 0.594734] . ( 7 sec) [ -2886.8391] [ 341] [depth= 4] . ( 8 sec) [ -2886.8155] [ 341] [depth= 1] . ( 9 sec) [ -2886.7785] [ 341] [depth= 1] . ( 9 sec) [ -2886.6492] [ 341] [depth= 1] . ( 11 sec) [ -2884.8502] [ 340] [depth= 1] . ( 13 sec) [ -2883.4882] [ 340] [depth= 1] . ( 15 sec) [ -2882.7987] [Branch lengths ] . ( 15 sec) [ -2882.7961] [Alpha ][ 0.602011] . ( 27 sec) [ -2882.7919] [Branch lengths ] . ( 27 sec) [ -2882.7919] [Topology ] . ( 27 sec) [ -2882.7918] [Topology ] . ( 27 sec) [ -2882.7918] [Alpha ][ 0.602011] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2882.791803. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4206.0305] [Alpha ][ 0.500960] . ( 0 sec) [ -4103.0255] [ 389] [depth= 6] . ( 0 sec) [ -3713.2807] [ 384] [depth= 4] . ( 0 sec) [ -3362.3703] [ 382] [depth= 2] . ( 0 sec) [ -3354.6411] [ 376] [depth= 1] . ( 0 sec) [ -3282.1272] [ 375] [depth= 3] . ( 1 sec) [ -3212.3529] [ 380] [depth= 1] . ( 1 sec) [ -3128.0585] [ 380] [depth= 1] . ( 1 sec) [ -3099.6898] [ 378] [depth= 2] . ( 1 sec) [ -3089.6940] [ 380] [depth= 1] . ( 1 sec) [ -2983.4186] [ 377] [depth= 1] . ( 2 sec) [ -2935.5233] [ 349] [depth= 4] . ( 2 sec) [ -2930.5232] [ 348] [depth= 1] . ( 2 sec) [ -2915.3642] [ 346] [depth= 4] . ( 2 sec) [ -2911.9815] [ 345] [depth= 1] . ( 3 sec) [ -2898.4671] [ 346] [depth= 1] . ( 3 sec) [ -2895.9082] [ 347] [depth= 1] . ( 3 sec) [ -2892.2211] [ 348] [depth= 4] . ( 4 sec) [ -2890.9867] [ 344] [depth= 3] . ( 4 sec) [ -2888.9790] [ 342] [depth= 2] . ( 4 sec) [ -2887.7696] [Branch lengths ] . ( 4 sec) [ -2887.2448] [Alpha ][ 0.590238] . ( 7 sec) [ -2883.6813] [ 340] [depth= 3] . ( 9 sec) [ -2883.3238] [ 340] [depth= 1] . ( 9 sec) [ -2883.2692] [ 340] [depth= 1] . ( 12 sec) [ -2883.2375] [ 340] [depth= 1] . ( 12 sec) [ -2883.1611] [ 340] [depth= 1] . ( 14 sec) [ -2882.8003] [Branch lengths ] . ( 14 sec) [ -2882.7934] [Alpha ][ 0.601505] . ( 26 sec) [ -2882.7918] [Branch lengths ] . ( 26 sec) [ -2882.7918] [Topology ] . ( 26 sec) [ -2882.7918] [Topology ] . ( 26 sec) [ -2882.7918] [Alpha ][ 0.601505] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2882.791793. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2896.3161] [Alpha ][ 0.545545] . ( 0 sec) [ -2896.3161] [Topology ] . ( 0 sec) [ -2884.4474] [Topology ] . ( 1 sec) [ -2883.2543] [Topology ] . ( 1 sec) [ -2883.0321] [Topology ] . ( 2 sec) [ -2882.9824] [Topology ] . ( 2 sec) [ -2882.9702] [Topology ] . ( 2 sec) [ -2882.9670] [Topology ] . ( 3 sec) [ -2882.9662] [Topology ] . Checking for NNIs, optimizing five branches... . ( 5 sec) [ -2882.7993] [Alpha ][ 0.599536] . ( 5 sec) [ -2882.7993] [Topology ] . ( 6 sec) [ -2882.7935] [Topology ] . ( 6 sec) [ -2882.7925] [Topology ] . ( 6 sec) [ -2882.7922] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -2882.7920] [Alpha ][ 0.601553] . ( 9 sec) [ -2882.7920] [Topology ] . ( 9 sec) [ -2882.7919] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 14 sec) [ -2896.3161] [Alpha ][ 0.545545] . ( 19 sec) [ -2894.0578] [ 343] [depth= 1] . ( 19 sec) [ -2893.9152] [ 343] [depth= 1] . ( 19 sec) [ -2892.6800] [ 342] [depth= 1] . ( 19 sec) [ -2891.2091] [ 342] [depth= 1] . ( 21 sec) [ -2888.7481] [ 340] [depth= 1] . ( 22 sec) [ -2888.3811] [ 340] [depth= 1] . ( 23 sec) [ -2888.2782] [ 340] [depth= 1] . ( 24 sec) [ -2883.4145] [Branch lengths ] . ( 24 sec) [ -2883.3102] [Alpha ][ 0.588414] . ( 28 sec) [ -2883.2662] [ 340] [depth= 1] . ( 35 sec) [ -2882.8179] [Branch lengths ] . ( 35 sec) [ -2882.8102] [Alpha ][ 0.600382] . ( 35 sec) [ -2882.8102] [Topology ] . ( 36 sec) [ -2882.7951] [Topology ] . ( 36 sec) [ -2882.7927] [Topology ] . ( 36 sec) [ -2882.7921] [Topology ] . ( 36 sec) [ -2882.7920] [Alpha ][ 0.601526] . ( 36 sec) [ -2882.7920] [Topology ] . ( 37 sec) [ -2882.7919] [Topology ] . ( 37 sec) [ -2882.7919] [Alpha ][ 0.601526] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2882.791948 . Log likelihood obtained after SPR moves : -2882.791868 . Log likelihood of the current tree: -2882.791868. . Printing the most likely tree in file 'proteic_M1384_11x391_2003.phy_phyml_tree.txt'... . Best log likelihood : -2882.791793 . Time used 0h0m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 169.11user 0.00system 2:51.32elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps