.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2640_18x243_2006.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... . 160 patterns found. (out of a total of 243 sites) . 99 sites without polymorphism (40.74%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4480.4949] [Alpha ][ 0.500960] . ( 0 sec) [ -3564.0827] [ 490] [depth= 7] . ( 0 sec) [ -3358.8036] [ 472] [depth= 6] . ( 0 sec) [ -3268.9808] [ 464] [depth= 5] . ( 0 sec) [ -3212.9238] [ 448] [depth= 1] . ( 1 sec) [ -3188.1944] [ 445] [depth= 5] . ( 1 sec) [ -3097.1074] [ 436] [depth= 4] . ( 1 sec) [ -3064.1239] [ 434] [depth= 2] . ( 1 sec) [ -3061.8599] [ 433] [depth= 1] . ( 1 sec) [ -3048.3084] [ 431] [depth= 1] . ( 1 sec) [ -3020.1212] [ 423] [depth= 1] . ( 1 sec) [ -2905.1352] [ 402] [depth= 5] . ( 2 sec) [ -2803.0271] [ 374] [depth= 4] . ( 2 sec) [ -2776.8551] [ 377] [depth= 7] . ( 2 sec) [ -2769.9596] [ 379] [depth= 4] . ( 2 sec) [ -2752.5754] [ 375] [depth= 1] . ( 2 sec) [ -2732.7032] [ 372] [depth= 1] . ( 2 sec) [ -2716.5413] [ 373] [depth= 1] . ( 2 sec) [ -2696.7989] [ 363] [depth= 5] . ( 2 sec) [ -2658.4971] [ 350] [depth= 1] . ( 3 sec) [ -2654.9436] [ 351] [depth= 1] . ( 3 sec) [ -2591.5997] [ 337] [depth= 2] . ( 3 sec) [ -2591.3527] [ 336] [depth= 1] . ( 3 sec) [ -2577.4175] [ 337] [depth= 1] . ( 4 sec) [ -2562.8870] [ 333] [depth= 2] . ( 4 sec) [ -2551.3155] [ 330] [depth= 2] . ( 4 sec) [ -2540.3692] [ 328] [depth= 1] . ( 7 sec) [ -2540.3519] [ 328] [depth= 1] . ( 7 sec) [ -2520.5460] [Branch lengths ] . ( 7 sec) [ -2511.6476] [Alpha ][ 1.000090] . ( 20 sec) [ -2511.0190] [Branch lengths ] . ( 20 sec) [ -2511.0190] [Topology ] . ( 21 sec) [ -2510.9926] [Topology ] . ( 21 sec) [ -2510.9874] [Topology ] . ( 22 sec) [ -2510.9859] [Topology ] . ( 23 sec) [ -2510.9855] [Topology ] . ( 23 sec) [ -2510.7884] [Alpha ][ 1.133434] . ( 23 sec) [ -2510.7884] [Topology ] . ( 23 sec) [ -2510.7764] [Topology ] . ( 24 sec) [ -2510.7736] [Topology ] . ( 25 sec) [ -2510.7729] [Topology ] . ( 25 sec) [ -2510.7723] [Alpha ][ 1.141326] . ( 25 sec) [ -2510.7723] [Topology ] . ( 26 sec) [ -2510.7719] [Topology ] . ( 26 sec) [ -2510.7719] [Alpha ][ 1.142467] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2510.771921. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4478.4088] [Alpha ][ 0.500960] . ( 0 sec) [ -4375.8912] [ 494] [depth= 6] . ( 0 sec) [ -3513.5143] [ 482] [depth= 6] . ( 0 sec) [ -3495.6952] [ 474] [depth= 1] . ( 0 sec) [ -3424.3723] [ 471] [depth= 2] . ( 0 sec) [ -3400.6820] [ 456] [depth= 1] . ( 0 sec) [ -3378.2861] [ 455] [depth= 1] . ( 1 sec) [ -3362.9668] [ 450] [depth= 2] . ( 1 sec) [ -3294.2210] [ 448] [depth= 3] . ( 1 sec) [ -3271.0615] [ 436] [depth= 5] . ( 1 sec) [ -3232.9660] [ 435] [depth= 1] . ( 1 sec) [ -3052.1527] [ 416] [depth= 9] . ( 1 sec) [ -2985.9512] [ 414] [depth= 3] . ( 1 sec) [ -2957.7769] [ 407] [depth= 1] . ( 2 sec) [ -2896.2536] [ 390] [depth= 4] . ( 2 sec) [ -2886.7291] [ 387] [depth= 1] . ( 2 sec) [ -2826.7373] [ 375] [depth= 4] . ( 2 sec) [ -2798.5273] [ 363] [depth= 5] . ( 2 sec) [ -2722.0127] [ 361] [depth= 3] . ( 3 sec) [ -2716.7473] [ 366] [depth= 1] . ( 3 sec) [ -2674.7030] [ 355] [depth= 3] . ( 3 sec) [ -2646.3313] [ 348] [depth= 1] . ( 3 sec) [ -2641.6897] [ 348] [depth= 3] . ( 3 sec) [ -2631.6171] [ 345] [depth= 3] . ( 3 sec) [ -2631.3743] [ 349] [depth= 2] . ( 3 sec) [ -2604.6603] [ 349] [depth= 1] . ( 4 sec) [ -2601.7718] [ 347] [depth= 1] . ( 4 sec) [ -2587.5205] [ 343] [depth= 1] . ( 4 sec) [ -2573.0023] [ 342] [depth= 2] . ( 4 sec) [ -2572.4948] [ 342] [depth= 1] . ( 4 sec) [ -2569.6189] [ 337] [depth= 2] . ( 5 sec) [ -2566.8251] [ 339] [depth= 1] . ( 6 sec) [ -2540.6327] [ 329] [depth= 1] . ( 6 sec) [ -2531.4711] [Branch lengths ] . ( 6 sec) [ -2524.0507] [Alpha ][ 0.989033] . ( 7 sec) [ -2513.7938] [ 328] [depth= 2] . ( 7 sec) [ -2513.7731] [ 328] [depth= 1] . ( 7 sec) [ -2512.7417] [ 328] [depth= 1] . ( 13 sec) [ -2512.7228] [ 328] [depth= 1] . ( 15 sec) [ -2512.7074] [ 328] [depth= 1] . ( 17 sec) [ -2511.0976] [Branch lengths ] . ( 18 sec) [ -2510.9059] [Alpha ][ 1.119330] . ( 30 sec) [ -2510.7849] [Branch lengths ] . ( 30 sec) [ -2510.7849] [Topology ] . ( 31 sec) [ -2510.7781] [Topology ] . ( 32 sec) [ -2510.7770] [Topology ] . ( 32 sec) [ -2510.7768] [Topology ] . ( 32 sec) [ -2510.7723] [Alpha ][ 1.140674] . ( 32 sec) [ -2510.7723] [Topology ] . ( 33 sec) [ -2510.7719] [Topology ] . ( 33 sec) [ -2510.7719] [Alpha ][ 1.141814] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2510.771920. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4845.5118] [Alpha ][ 0.500960] . ( 0 sec) [ -4744.2194] [ 461] [depth= 2] . ( 0 sec) [ -4684.8198] [ 455] [depth= 2] . ( 1 sec) [ -4673.6744] [ 455] [depth= 6] . ( 1 sec) [ -4573.1506] [ 430] [depth= 5] . ( 1 sec) [ -4528.4159] [ 423] [depth= 2] . ( 1 sec) [ -4520.1443] [ 422] [depth= 3] . ( 1 sec) [ -4496.7531] [ 417] [depth= 1] . ( 1 sec) [ -4493.8637] [ 417] [depth= 1] . ( 1 sec) [ -4459.0309] [ 412] [depth= 4] . ( 1 sec) [ -4418.6180] [ 404] [depth= 3] . ( 1 sec) [ -4301.6919] [ 383] [depth= 2] . ( 2 sec) [ -3035.4743] [ 376] [depth= 5] . ( 2 sec) [ -3007.0716] [ 373] [depth= 4] . ( 2 sec) [ -2992.0277] [ 371] [depth= 6] . ( 2 sec) [ -2917.1309] [ 367] [depth= 2] . ( 3 sec) [ -2906.5584] [ 365] [depth= 5] . ( 3 sec) [ -2904.6798] [ 365] [depth= 1] . ( 3 sec) [ -2880.7482] [ 356] [depth= 1] . ( 3 sec) [ -2859.8581] [ 353] [depth= 2] . ( 4 sec) [ -2794.7026] [ 336] [depth= 2] . ( 4 sec) [ -2794.5751] [ 336] [depth= 1] . ( 4 sec) [ -2766.6880] [ 336] [depth= 2] . ( 4 sec) [ -2761.7554] [ 339] [depth= 1] . ( 5 sec) [ -2732.6646] [ 329] [depth= 2] . ( 5 sec) [ -2732.5947] [ 329] [depth= 1] . ( 5 sec) [ -2720.7317] [ 330] [depth= 1] . ( 6 sec) [ -2714.7783] [ 328] [depth= 1] . ( 6 sec) [ -2710.2616] [ 328] [depth= 1] . ( 6 sec) [ -2553.0498] [ 332] [depth= 1] . ( 7 sec) [ -2526.3269] [ 328] [depth= 1] . ( 7 sec) [ -2520.2310] [Branch lengths ] . ( 7 sec) [ -2512.5756] [Alpha ][ 1.000148] . ( 7 sec) [ -2512.5361] [ 328] [depth= 1] . ( 19 sec) [ -2511.0880] [Branch lengths ] . ( 19 sec) [ -2510.9425] [Alpha ][ 1.114563] . ( 32 sec) [ -2510.7857] [Branch lengths ] . ( 32 sec) [ -2510.7857] [Topology ] . ( 33 sec) [ -2510.7803] [Topology ] . ( 33 sec) [ -2510.7793] [Topology ] . ( 34 sec) [ -2510.7790] [Topology ] . ( 34 sec) [ -2510.7725] [Alpha ][ 1.140482] . ( 34 sec) [ -2510.7725] [Topology ] . ( 35 sec) [ -2510.7719] [Topology ] . ( 35 sec) [ -2510.7719] [Alpha ][ 1.141622] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2510.771853. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3682.7990] [Alpha ][ 0.500960] . ( 0 sec) [ -3593.8004] [ 484] [depth= 3] . ( 0 sec) [ -3571.3806] [ 477] [depth= 4] . ( 0 sec) [ -3570.5636] [ 473] [depth= 4] . ( 0 sec) [ -3560.4936] [ 477] [depth= 1] . ( 0 sec) [ -3556.5733] [ 473] [depth= 1] . ( 0 sec) [ -3522.1637] [ 475] [depth= 1] . ( 1 sec) [ -3514.1653] [ 471] [depth= 1] . ( 1 sec) [ -3451.4596] [ 456] [depth= 7] . ( 1 sec) [ -3385.4242] [ 445] [depth= 4] . ( 1 sec) [ -3271.5551] [ 432] [depth= 5] . ( 1 sec) [ -3224.6529] [ 432] [depth= 1] . ( 1 sec) [ -3211.4046] [ 432] [depth= 1] . ( 1 sec) [ -3127.5777] [ 405] [depth= 5] . ( 1 sec) [ -3126.7473] [ 405] [depth= 1] . ( 2 sec) [ -3123.6196] [ 404] [depth= 1] . ( 2 sec) [ -3123.4701] [ 404] [depth= 1] . ( 2 sec) [ -2916.1764] [ 367] [depth= 8] . ( 2 sec) [ -2812.9888] [ 353] [depth= 3] . ( 2 sec) [ -2789.2477] [ 354] [depth= 1] . ( 2 sec) [ -2784.3227] [ 353] [depth= 1] . ( 3 sec) [ -2759.8302] [ 357] [depth= 1] . ( 3 sec) [ -2722.3404] [ 349] [depth= 3] . ( 3 sec) [ -2608.0245] [ 343] [depth= 1] . ( 3 sec) [ -2607.8525] [ 343] [depth= 1] . ( 4 sec) [ -2573.5360] [ 331] [depth= 4] . ( 4 sec) [ -2571.8688] [ 331] [depth= 1] . ( 4 sec) [ -2568.2903] [ 337] [depth= 1] . ( 4 sec) [ -2563.1681] [ 335] [depth= 1] . ( 5 sec) [ -2549.2660] [ 332] [depth= 1] . ( 5 sec) [ -2530.8929] [ 328] [depth= 1] . ( 5 sec) [ -2530.4958] [ 328] [depth= 1] . ( 6 sec) [ -2524.2247] [Branch lengths ] . ( 6 sec) [ -2516.8354] [Alpha ][ 0.996854] . ( 10 sec) [ -2516.7642] [ 328] [depth= 1] . ( 12 sec) [ -2515.6997] [ 328] [depth= 1] . ( 17 sec) [ -2511.1879] [Branch lengths ] . ( 18 sec) [ -2511.0256] [Alpha ][ 1.117263] . ( 30 sec) [ -2510.7825] [Branch lengths ] . ( 30 sec) [ -2510.7825] [Topology ] . ( 30 sec) [ -2510.7783] [Topology ] . ( 31 sec) [ -2510.7778] [Topology ] . ( 31 sec) [ -2510.7725] [Alpha ][ 1.140353] . ( 31 sec) [ -2510.7725] [Topology ] . ( 32 sec) [ -2510.7719] [Topology ] . ( 32 sec) [ -2510.7719] [Alpha ][ 1.141542] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2510.771918. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4320.9244] [Alpha ][ 0.500960] . ( 0 sec) [ -4249.7031] [ 471] [depth= 2] . ( 0 sec) [ -4170.6436] [ 460] [depth= 4] . ( 0 sec) [ -4152.8031] [ 460] [depth= 3] . ( 1 sec) [ -4078.6363] [ 443] [depth= 7] . ( 1 sec) [ -4054.1027] [ 436] [depth= 1] . ( 1 sec) [ -3993.4860] [ 432] [depth= 1] . ( 1 sec) [ -3914.2578] [ 412] [depth= 1] . ( 1 sec) [ -3900.1871] [ 410] [depth= 1] . ( 1 sec) [ -3892.8332] [ 411] [depth= 1] . ( 1 sec) [ -3884.2523] [ 411] [depth= 1] . ( 1 sec) [ -3878.0223] [ 406] [depth= 2] . ( 2 sec) [ -3805.5827] [ 392] [depth= 5] . ( 2 sec) [ -3787.0430] [ 386] [depth= 1] . ( 2 sec) [ -3031.7167] [ 374] [depth= 2] . ( 2 sec) [ -2976.7857] [ 374] [depth= 1] . ( 2 sec) [ -2924.9663] [ 370] [depth= 2] . ( 2 sec) [ -2924.7977] [ 370] [depth= 1] . ( 2 sec) [ -2873.8842] [ 361] [depth= 1] . ( 2 sec) [ -2785.6979] [ 358] [depth= 2] . ( 3 sec) [ -2771.8800] [ 354] [depth= 1] . ( 3 sec) [ -2749.5937] [ 346] [depth= 1] . ( 3 sec) [ -2732.2653] [ 341] [depth= 2] . ( 3 sec) [ -2723.2327] [ 339] [depth= 1] . ( 3 sec) [ -2721.1216] [ 339] [depth= 1] . ( 3 sec) [ -2718.6973] [ 342] [depth= 1] . ( 4 sec) [ -2711.0507] [ 339] [depth= 1] . ( 4 sec) [ -2710.0794] [ 339] [depth= 1] . ( 4 sec) [ -2568.9077] [ 337] [depth= 1] . ( 5 sec) [ -2557.5661] [ 339] [depth= 1] . ( 5 sec) [ -2557.5542] [ 339] [depth= 1] . ( 5 sec) [ -2527.3491] [ 328] [depth= 4] . ( 5 sec) [ -2520.3043] [Branch lengths ] . ( 6 sec) [ -2512.2673] [Alpha ][ 1.000155] . ( 10 sec) [ -2512.2490] [ 328] [depth= 1] . ( 11 sec) [ -2512.2343] [ 328] [depth= 1] . ( 11 sec) [ -2512.2221] [ 328] [depth= 1] . ( 18 sec) [ -2511.0547] [Branch lengths ] . ( 19 sec) [ -2510.9049] [Alpha ][ 1.116140] . ( 31 sec) [ -2510.7829] [Branch lengths ] . ( 31 sec) [ -2510.7829] [Topology ] . ( 32 sec) [ -2510.7790] [Topology ] . ( 32 sec) [ -2510.7783] [Topology ] . ( 32 sec) [ -2510.7727] [Alpha ][ 1.140090] . ( 32 sec) [ -2510.7727] [Topology ] . ( 33 sec) [ -2510.7719] [Topology ] . ( 33 sec) [ -2510.7719] [Alpha ][ 1.141382] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2510.771923. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2517.5928] [Alpha ][ 1.082783] . ( 0 sec) [ -2517.5928] [Topology ] . ( 1 sec) [ -2511.5164] [Topology ] . ( 2 sec) [ -2510.9156] [Topology ] . ( 2 sec) [ -2510.8267] [Topology ] . ( 3 sec) [ -2510.8104] [Topology ] . ( 4 sec) [ -2510.8068] [Topology ] . ( 4 sec) [ -2510.8060] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -2510.7749] [Alpha ][ 1.138493] . ( 9 sec) [ -2510.7749] [Topology ] . ( 10 sec) [ -2510.7726] [Topology ] . ( 10 sec) [ -2510.7720] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -2510.7719] [Alpha ][ 1.141544] . ( 15 sec) [ -2510.7719] [Topology ] . ( 16 sec) [ -2510.7717] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 25 sec) [ -2517.5928] [Alpha ][ 1.082783] . ( 26 sec) [ -2517.5001] [ 328] [depth= 1] . ( 36 sec) [ -2517.4550] [ 328] [depth= 1] . ( 37 sec) [ -2516.4768] [ 328] [depth= 1] . ( 37 sec) [ -2510.8754] [Branch lengths ] . ( 37 sec) [ -2510.8510] [Alpha ][ 1.132562] . ( 49 sec) [ -2510.7744] [Branch lengths ] . ( 49 sec) [ -2510.7744] [Topology ] . ( 50 sec) [ -2510.7729] [Topology ] . ( 51 sec) [ -2510.7727] [Topology ] . ( 51 sec) [ -2510.7718] [Alpha ][ 1.142182] . ( 51 sec) [ -2510.7718] [Topology ] . ( 51 sec) [ -2510.7717] [Topology ] . ( 52 sec) [ -2510.7717] [Alpha ][ 1.142182] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2510.771729 . Log likelihood obtained after SPR moves : -2510.771721 . Log likelihood of the current tree: -2510.771721. . Printing the most likely tree in file 'proteic_M2640_18x243_2006.phy_phyml_tree.txt'... . Best log likelihood : -2510.771721 . Time used 0h0m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 236.65user 0.00system 4:00.87elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps