.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1989_18x173_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 : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 7 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 139 patterns found. (out of a total of 173 sites) . 46 sites without polymorphism (26.59%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4786.3076] [Alpha ][ 0.500960] . ( 0 sec) [ -4674.8792] [ 782] [depth= 4] . ( 0 sec) [ -4454.6349] [ 755] [depth= 4] . ( 0 sec) [ -4383.2956] [ 754] [depth= 1] . ( 0 sec) [ -4310.1712] [ 742] [depth= 3] . ( 1 sec) [ -4225.6998] [ 719] [depth= 3] . ( 1 sec) [ -4182.2787] [ 710] [depth= 1] . ( 1 sec) [ -4118.6781] [ 696] [depth= 5] . ( 1 sec) [ -4037.9738] [ 691] [depth= 3] . ( 1 sec) [ -4025.0064] [ 693] [depth= 2] . ( 1 sec) [ -3997.1601] [ 692] [depth= 5] . ( 1 sec) [ -3976.3557] [ 692] [depth= 1] . ( 1 sec) [ -3973.7831] [ 695] [depth= 1] . ( 1 sec) [ -3968.9584] [ 684] [depth= 3] . ( 2 sec) [ -3937.2706] [ 666] [depth= 3] . ( 2 sec) [ -3801.1891] [ 659] [depth= 2] . ( 2 sec) [ -3770.7946] [ 654] [depth= 3] . ( 2 sec) [ -3586.9744] [ 648] [depth= 3] . ( 2 sec) [ -3570.1719] [ 652] [depth= 1] . ( 2 sec) [ -3426.2700] [ 634] [depth= 1] . ( 2 sec) [ -3388.1991] [ 622] [depth= 5] . ( 2 sec) [ -3349.9325] [ 616] [depth= 2] . ( 3 sec) [ -3347.2996] [ 616] [depth= 2] . ( 3 sec) [ -3290.9927] [ 603] [depth= 3] . ( 3 sec) [ -3288.0492] [ 604] [depth= 2] . ( 3 sec) [ -3285.0709] [ 605] [depth= 1] . ( 3 sec) [ -3282.5958] [ 605] [depth= 1] . ( 3 sec) [ -3271.9308] [ 597] [depth= 1] . ( 3 sec) [ -3271.7839] [ 600] [depth= 1] . ( 4 sec) [ -3271.3290] [ 600] [depth= 1] . ( 4 sec) [ -3271.1745] [ 600] [depth= 1] . ( 4 sec) [ -3271.0708] [ 600] [depth= 1] . ( 4 sec) [ -3264.0288] [ 598] [depth= 1] . ( 4 sec) [ -3254.2231] [ 598] [depth= 1] . ( 4 sec) [ -3238.4400] [ 598] [depth= 1] . ( 4 sec) [ -3236.8738] [ 598] [depth= 1] . ( 4 sec) [ -3235.8011] [ 597] [depth= 1] . ( 4 sec) [ -3226.1413] [ 594] [depth= 1] . ( 5 sec) [ -3199.8171] [Branch lengths ] . ( 5 sec) [ -3196.4596] [Alpha ][ 0.700230] . ( 5 sec) [ -3196.3576] [ 594] [depth= 1] . ( 6 sec) [ -3195.4624] [ 594] [depth= 1] . ( 6 sec) [ -3194.7205] [ 593] [depth= 1] . ( 7 sec) [ -3190.0041] [ 591] [depth= 2] . ( 7 sec) [ -3189.9702] [ 591] [depth= 1] . ( 8 sec) [ -3187.3961] [ 590] [depth= 1] . ( 9 sec) [ -3186.6246] [ 587] [depth= 1] . ( 10 sec) [ -3186.6094] [ 587] [depth= 1] . ( 11 sec) [ -3186.5791] [ 587] [depth= 1] . ( 11 sec) [ -3186.5270] [ 587] [depth= 1] . ( 11 sec) [ -3186.3978] [ 587] [depth= 1] . ( 11 sec) [ -3186.3604] [ 587] [depth= 1] . ( 13 sec) [ -3180.9776] [Branch lengths ] . ( 13 sec) [ -3180.7307] [Alpha ][ 0.767901] . ( 16 sec) [ -3180.7050] [ 587] [depth= 1] . ( 22 sec) [ -3180.1340] [Branch lengths ] . ( 22 sec) [ -3180.1152] [Alpha ][ 0.787399] . ( 22 sec) [ -3180.1152] [Topology ] . ( 23 sec) [ -3180.0055] [Topology ] . ( 23 sec) [ -3179.9605] [Topology ] . ( 24 sec) [ -3179.9363] [Topology ] . ( 25 sec) [ -3179.9227] [Topology ] . ( 25 sec) [ -3179.9148] [Topology ] . ( 26 sec) [ -3179.9103] [Topology ] . ( 26 sec) [ -3179.9053] [Alpha ][ 0.797922] . ( 26 sec) [ -3179.9053] [Topology ] . ( 26 sec) [ -3179.9017] [Topology ] . ( 27 sec) [ -3179.8997] [Topology ] . ( 28 sec) [ -3179.8985] [Topology ] . ( 28 sec) [ -3179.8978] [Topology ] . ( 28 sec) [ -3179.8977] [Alpha ][ 0.799382] . ( 28 sec) [ -3179.8977] [Topology ] . ( 29 sec) [ -3179.8973] [Topology ] . ( 29 sec) [ -3179.8973] [Alpha ][ 0.799382] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897255. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4883.7147] [Alpha ][ 0.500960] . ( 0 sec) [ -4842.4229] [ 833] [depth= 6] . ( 1 sec) [ -4698.5005] [ 793] [depth= 5] . ( 1 sec) [ -4534.9769] [ 788] [depth= 2] . ( 1 sec) [ -4440.4924] [ 776] [depth= 5] . ( 1 sec) [ -4396.7142] [ 766] [depth= 1] . ( 1 sec) [ -4294.3353] [ 749] [depth= 6] . ( 1 sec) [ -4215.8284] [ 739] [depth= 1] . ( 1 sec) [ -4115.5483] [ 725] [depth= 3] . ( 1 sec) [ -3948.4222] [ 695] [depth= 1] . ( 1 sec) [ -3867.4915] [ 688] [depth= 4] . ( 1 sec) [ -3739.4139] [ 672] [depth= 2] . ( 2 sec) [ -3719.5338] [ 671] [depth= 2] . ( 2 sec) [ -3676.6595] [ 664] [depth= 3] . ( 2 sec) [ -3596.9371] [ 661] [depth= 2] . ( 2 sec) [ -3587.5746] [ 660] [depth= 1] . ( 2 sec) [ -3584.4657] [ 660] [depth= 1] . ( 2 sec) [ -3577.3305] [ 660] [depth= 1] . ( 2 sec) [ -3406.5653] [ 631] [depth= 2] . ( 3 sec) [ -3398.6169] [ 631] [depth= 1] . ( 3 sec) [ -3391.1078] [ 631] [depth= 2] . ( 3 sec) [ -3390.4047] [ 632] [depth= 1] . ( 3 sec) [ -3390.3156] [ 632] [depth= 1] . ( 3 sec) [ -3390.1485] [ 634] [depth= 1] . ( 3 sec) [ -3358.7315] [ 636] [depth= 2] . ( 4 sec) [ -3358.7188] [ 635] [depth= 2] . ( 4 sec) [ -3355.5962] [ 636] [depth= 2] . ( 4 sec) [ -3348.4421] [ 624] [depth= 1] . ( 4 sec) [ -3348.2971] [ 624] [depth= 1] . ( 4 sec) [ -3330.1684] [ 619] [depth= 1] . ( 4 sec) [ -3309.7556] [ 608] [depth= 4] . ( 4 sec) [ -3300.2062] [ 607] [depth= 6] . ( 4 sec) [ -3285.9462] [ 618] [depth= 1] . ( 5 sec) [ -3279.5254] [ 610] [depth= 1] . ( 5 sec) [ -3272.9987] [ 599] [depth= 1] . ( 5 sec) [ -3262.6049] [ 597] [depth= 1] . ( 5 sec) [ -3252.5285] [ 597] [depth= 1] . ( 5 sec) [ -3250.8182] [ 598] [depth= 1] . ( 5 sec) [ -3250.6533] [ 598] [depth= 1] . ( 6 sec) [ -3222.2103] [Branch lengths ] . ( 6 sec) [ -3219.6173] [Alpha ][ 0.668069] . ( 6 sec) [ -3219.5415] [ 598] [depth= 1] . ( 6 sec) [ -3216.3365] [ 600] [depth= 1] . ( 7 sec) [ -3215.4304] [ 599] [depth= 1] . ( 8 sec) [ -3206.5720] [ 587] [depth= 2] . ( 8 sec) [ -3206.0587] [ 589] [depth= 2] . ( 8 sec) [ -3205.9922] [ 589] [depth= 1] . ( 8 sec) [ -3205.8900] [ 589] [depth= 1] . ( 9 sec) [ -3203.7550] [ 586] [depth= 1] . ( 9 sec) [ -3200.1151] [ 589] [depth= 1] . ( 10 sec) [ -3194.2323] [ 586] [depth= 1] . ( 10 sec) [ -3193.4161] [ 587] [depth= 1] . ( 10 sec) [ -3193.3065] [ 587] [depth= 1] . ( 11 sec) [ -3193.2355] [ 587] [depth= 1] . ( 12 sec) [ -3191.8341] [ 590] [depth= 1] . ( 12 sec) [ -3191.0755] [ 595] [depth= 2] . ( 13 sec) [ -3188.2710] [ 596] [depth= 1] . ( 14 sec) [ -3187.5590] [ 590] [depth= 1] . ( 15 sec) [ -3187.4825] [ 590] [depth= 1] . ( 15 sec) [ -3183.2791] [Branch lengths ] . ( 15 sec) [ -3182.4384] [Alpha ][ 0.789845] . ( 17 sec) [ -3181.0885] [ 587] [depth= 1] . ( 24 sec) [ -3179.9817] [Branch lengths ] . ( 24 sec) [ -3179.9775] [Alpha ][ 0.799521] . ( 34 sec) [ -3179.9069] [Branch lengths ] . ( 34 sec) [ -3179.9069] [Topology ] . ( 35 sec) [ -3179.9006] [Topology ] . ( 35 sec) [ -3179.8986] [Topology ] . ( 36 sec) [ -3179.8977] [Topology ] . ( 36 sec) [ -3179.8976] [Alpha ][ 0.800320] . ( 36 sec) [ -3179.8976] [Topology ] . ( 36 sec) [ -3179.8972] [Topology ] . ( 37 sec) [ -3179.8972] [Alpha ][ 0.800320] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897183. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4812.2103] [Alpha ][ 0.500960] . ( 1 sec) [ -4589.0716] [ 793] [depth= 3] . ( 1 sec) [ -4336.3859] [ 749] [depth= 6] . ( 1 sec) [ -4286.5372] [ 740] [depth= 1] . ( 1 sec) [ -4282.4597] [ 737] [depth= 1] . ( 1 sec) [ -4210.2998] [ 717] [depth= 1] . ( 1 sec) [ -4137.2369] [ 711] [depth= 2] . ( 1 sec) [ -4113.9835] [ 709] [depth= 1] . ( 1 sec) [ -3998.4245] [ 703] [depth= 5] . ( 2 sec) [ -3986.7103] [ 703] [depth= 1] . ( 2 sec) [ -3962.3852] [ 692] [depth= 1] . ( 2 sec) [ -3921.2605] [ 688] [depth= 2] . ( 2 sec) [ -3766.1723] [ 677] [depth= 1] . ( 2 sec) [ -3629.3202] [ 650] [depth= 2] . ( 2 sec) [ -3507.1259] [ 644] [depth= 1] . ( 2 sec) [ -3483.5943] [ 644] [depth= 1] . ( 2 sec) [ -3473.8711] [ 644] [depth= 1] . ( 2 sec) [ -3466.2019] [ 647] [depth= 4] . ( 3 sec) [ -3432.6374] [ 638] [depth= 2] . ( 3 sec) [ -3401.9330] [ 636] [depth= 3] . ( 3 sec) [ -3361.1489] [ 622] [depth= 3] . ( 3 sec) [ -3336.3633] [ 619] [depth= 6] . ( 3 sec) [ -3279.0899] [ 606] [depth= 2] . ( 3 sec) [ -3277.3138] [ 606] [depth= 1] . ( 3 sec) [ -3277.2049] [ 606] [depth= 1] . ( 4 sec) [ -3272.8830] [ 607] [depth= 2] . ( 4 sec) [ -3265.4150] [ 605] [depth= 2] . ( 4 sec) [ -3245.8625] [ 596] [depth= 1] . ( 4 sec) [ -3242.0555] [ 596] [depth= 1] . ( 4 sec) [ -3241.1237] [ 596] [depth= 1] . ( 4 sec) [ -3232.7189] [ 591] [depth= 1] . ( 5 sec) [ -3231.8296] [ 590] [depth= 1] . ( 5 sec) [ -3231.7946] [ 590] [depth= 1] . ( 5 sec) [ -3228.0507] [ 590] [depth= 1] . ( 5 sec) [ -3221.7762] [ 593] [depth= 1] . ( 5 sec) [ -3221.7149] [ 593] [depth= 1] . ( 5 sec) [ -3200.8808] [Branch lengths ] . ( 5 sec) [ -3197.0264] [Alpha ][ 0.715935] . ( 6 sec) [ -3196.6517] [ 593] [depth= 2] . ( 7 sec) [ -3190.7497] [ 590] [depth= 4] . ( 7 sec) [ -3189.5580] [ 591] [depth= 2] . ( 8 sec) [ -3189.2289] [ 593] [depth= 2] . ( 10 sec) [ -3188.6987] [ 596] [depth= 1] . ( 12 sec) [ -3187.5204] [ 593] [depth= 1] . ( 14 sec) [ -3186.7171] [ 590] [depth= 1] . ( 15 sec) [ -3182.7553] [Branch lengths ] . ( 15 sec) [ -3182.5491] [Alpha ][ 0.778011] . ( 27 sec) [ -3182.2654] [Branch lengths ] . ( 27 sec) [ -3182.2654] [Topology ] . ( 28 sec) [ -3181.8243] [Topology ] . ( 28 sec) [ -3181.6745] [Topology ] . ( 29 sec) [ -3180.2152] [Topology ] . ( 29 sec) [ -3179.9903] [Topology ] . ( 30 sec) [ -3179.9424] [Topology ] . ( 30 sec) [ -3179.9278] [Topology ] . ( 31 sec) [ -3179.9227] [Topology ] . ( 32 sec) [ -3179.9207] [Topology ] . ( 32 sec) [ -3179.9198] [Topology ] . ( 32 sec) [ -3179.8980] [Alpha ][ 0.799168] . ( 32 sec) [ -3179.8980] [Topology ] . ( 33 sec) [ -3179.8972] [Topology ] . ( 33 sec) [ -3179.8971] [Alpha ][ 0.799968] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897145. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -5219.1402] [Alpha ][ 0.500960] . ( 1 sec) [ -4942.1831] [ 790] [depth= 3] . ( 1 sec) [ -4548.8783] [ 766] [depth= 7] . ( 1 sec) [ -4475.4973] [ 754] [depth= 1] . ( 1 sec) [ -4412.9606] [ 733] [depth= 2] . ( 1 sec) [ -4396.0560] [ 726] [depth= 1] . ( 1 sec) [ -4276.7611] [ 709] [depth= 2] . ( 1 sec) [ -4228.7272] [ 709] [depth= 1] . ( 2 sec) [ -4041.3175] [ 714] [depth= 1] . ( 2 sec) [ -3958.8104] [ 704] [depth= 2] . ( 2 sec) [ -3875.4981] [ 685] [depth= 6] . ( 2 sec) [ -3781.5028] [ 675] [depth= 2] . ( 2 sec) [ -3773.8467] [ 675] [depth= 1] . ( 2 sec) [ -3690.8181] [ 669] [depth= 3] . ( 2 sec) [ -3668.3618] [ 680] [depth= 1] . ( 2 sec) [ -3627.5506] [ 669] [depth= 3] . ( 2 sec) [ -3624.7202] [ 669] [depth= 1] . ( 3 sec) [ -3612.6058] [ 665] [depth= 3] . ( 3 sec) [ -3580.5348] [ 653] [depth= 3] . ( 3 sec) [ -3425.4534] [ 636] [depth= 5] . ( 3 sec) [ -3411.5852] [ 639] [depth= 2] . ( 3 sec) [ -3389.6632] [ 640] [depth= 3] . ( 3 sec) [ -3380.1004] [ 649] [depth= 7] . ( 3 sec) [ -3379.7949] [ 649] [depth= 1] . ( 3 sec) [ -3350.0238] [ 627] [depth= 5] . ( 4 sec) [ -3336.1213] [ 631] [depth= 1] . ( 4 sec) [ -3257.0272] [ 600] [depth= 8] . ( 4 sec) [ -3253.9446] [ 600] [depth= 1] . ( 4 sec) [ -3251.1136] [ 601] [depth= 1] . ( 4 sec) [ -3250.5344] [ 598] [depth= 1] . ( 4 sec) [ -3240.2847] [ 588] [depth= 2] . ( 5 sec) [ -3236.7615] [ 589] [depth= 1] . ( 5 sec) [ -3236.4301] [ 589] [depth= 1] . ( 5 sec) [ -3236.1889] [ 587] [depth= 1] . ( 5 sec) [ -3234.0603] [ 589] [depth= 3] . ( 5 sec) [ -3197.4162] [Branch lengths ] . ( 6 sec) [ -3193.2651] [Alpha ][ 0.724120] . ( 6 sec) [ -3193.2099] [ 588] [depth= 1] . ( 7 sec) [ -3193.0759] [ 589] [depth= 1] . ( 7 sec) [ -3192.6939] [ 592] [depth= 1] . ( 7 sec) [ -3192.3575] [ 590] [depth= 1] . ( 7 sec) [ -3191.0494] [ 587] [depth= 1] . ( 10 sec) [ -3190.2286] [ 588] [depth= 1] . ( 10 sec) [ -3185.2735] [ 587] [depth= 2] . ( 13 sec) [ -3181.7856] [Branch lengths ] . ( 13 sec) [ -3181.6647] [Alpha ][ 0.772310] . ( 22 sec) [ -3181.2261] [Branch lengths ] . ( 22 sec) [ -3181.2261] [Topology ] . ( 23 sec) [ -3181.0789] [Topology ] . ( 23 sec) [ -3180.5808] [Topology ] . ( 24 sec) [ -3180.2810] [Topology ] . ( 25 sec) [ -3180.1179] [Topology ] . ( 25 sec) [ -3180.0306] [Topology ] . ( 26 sec) [ -3179.9842] [Topology ] . ( 26 sec) [ -3179.9530] [Alpha ][ 0.797746] . ( 26 sec) [ -3179.9530] [Topology ] . ( 26 sec) [ -3179.9266] [Topology ] . ( 27 sec) [ -3179.9128] [Topology ] . ( 27 sec) [ -3179.9055] [Topology ] . ( 28 sec) [ -3179.9016] [Topology ] . ( 29 sec) [ -3179.8995] [Topology ] . ( 29 sec) [ -3179.8983] [Topology ] . ( 29 sec) [ -3179.8981] [Alpha ][ 0.799719] . ( 29 sec) [ -3179.8981] [Topology ] . ( 30 sec) [ -3179.8974] [Topology ] . ( 30 sec) [ -3179.8974] [Alpha ][ 0.799719] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897434. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -5058.8022] [Alpha ][ 0.500960] . ( 1 sec) [ -5015.5645] [ 817] [depth= 5] . ( 1 sec) [ -4847.4825] [ 793] [depth= 4] . ( 1 sec) [ -4737.7815] [ 780] [depth= 3] . ( 1 sec) [ -4641.4274] [ 778] [depth= 2] . ( 1 sec) [ -4547.4796] [ 761] [depth= 1] . ( 1 sec) [ -4348.5410] [ 753] [depth= 3] . ( 1 sec) [ -4308.1000] [ 734] [depth= 6] . ( 2 sec) [ -4216.3079] [ 744] [depth= 1] . ( 2 sec) [ -4212.5738] [ 743] [depth= 1] . ( 2 sec) [ -4067.2161] [ 716] [depth= 8] . ( 2 sec) [ -3838.9793] [ 682] [depth= 2] . ( 2 sec) [ -3835.9226] [ 682] [depth= 1] . ( 2 sec) [ -3752.7702] [ 670] [depth= 5] . ( 2 sec) [ -3693.3875] [ 667] [depth= 4] . ( 2 sec) [ -3597.9095] [ 664] [depth= 7] . ( 2 sec) [ -3578.8290] [ 657] [depth= 4] . ( 2 sec) [ -3534.9384] [ 650] [depth= 1] . ( 3 sec) [ -3534.4643] [ 649] [depth= 2] . ( 3 sec) [ -3524.5561] [ 649] [depth= 3] . ( 3 sec) [ -3449.3581] [ 635] [depth= 3] . ( 3 sec) [ -3431.8761] [ 621] [depth= 1] . ( 3 sec) [ -3398.3072] [ 617] [depth= 1] . ( 3 sec) [ -3330.9020] [ 608] [depth= 6] . ( 4 sec) [ -3329.4798] [ 620] [depth= 1] . ( 4 sec) [ -3317.3732] [ 620] [depth= 2] . ( 4 sec) [ -3316.3646] [ 624] [depth= 4] . ( 4 sec) [ -3304.3389] [ 627] [depth= 2] . ( 4 sec) [ -3294.0006] [ 617] [depth= 3] . ( 4 sec) [ -3270.8719] [ 604] [depth= 1] . ( 4 sec) [ -3268.9114] [ 604] [depth= 1] . ( 4 sec) [ -3257.5555] [ 605] [depth= 1] . ( 5 sec) [ -3252.1800] [ 604] [depth= 1] . ( 5 sec) [ -3250.8832] [ 605] [depth= 1] . ( 5 sec) [ -3249.9624] [ 602] [depth= 1] . ( 6 sec) [ -3249.0377] [ 607] [depth= 1] . ( 6 sec) [ -3244.2311] [ 611] [depth= 1] . ( 6 sec) [ -3241.9509] [ 609] [depth= 2] . ( 6 sec) [ -3240.6166] [ 606] [depth= 2] . ( 6 sec) [ -3240.5506] [ 607] [depth= 2] . ( 6 sec) [ -3239.8088] [ 607] [depth= 1] . ( 7 sec) [ -3209.6095] [Branch lengths ] . ( 7 sec) [ -3206.8028] [Alpha ][ 0.676684] . ( 7 sec) [ -3202.6147] [ 598] [depth= 1] . ( 7 sec) [ -3200.8713] [ 598] [depth= 1] . ( 8 sec) [ -3198.1802] [ 595] [depth= 3] . ( 8 sec) [ -3198.1377] [ 595] [depth= 1] . ( 9 sec) [ -3197.3833] [ 598] [depth= 1] . ( 9 sec) [ -3197.1446] [ 599] [depth= 1] . ( 10 sec) [ -3196.6293] [ 594] [depth= 2] . ( 11 sec) [ -3195.2038] [ 591] [depth= 1] . ( 11 sec) [ -3195.0981] [ 591] [depth= 1] . ( 11 sec) [ -3194.2915] [ 593] [depth= 1] . ( 12 sec) [ -3194.1439] [ 587] [depth= 2] . ( 12 sec) [ -3193.9601] [ 586] [depth= 1] . ( 13 sec) [ -3190.4710] [ 586] [depth= 1] . ( 14 sec) [ -3190.1407] [ 588] [depth= 1] . ( 15 sec) [ -3190.1278] [ 588] [depth= 1] . ( 15 sec) [ -3182.9191] [Branch lengths ] . ( 15 sec) [ -3182.2585] [Alpha ][ 0.785482] . ( 20 sec) [ -3182.1151] [ 586] [depth= 1] . ( 20 sec) [ -3181.4941] [ 587] [depth= 1] . ( 23 sec) [ -3181.4592] [ 587] [depth= 1] . ( 26 sec) [ -3179.9706] [Branch lengths ] . ( 26 sec) [ -3179.9627] [Alpha ][ 0.798766] . ( 35 sec) [ -3179.9017] [Branch lengths ] . ( 36 sec) [ -3179.9017] [Topology ] . ( 36 sec) [ -3179.8984] [Topology ] . ( 37 sec) [ -3179.8975] [Topology ] . ( 37 sec) [ -3179.8975] [Alpha ][ 0.799574] . ( 37 sec) [ -3179.8975] [Topology ] . ( 37 sec) [ -3179.8971] [Topology ] . ( 37 sec) [ -3179.8971] [Alpha ][ 0.799574] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897113. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3205.9405] [Alpha ][ 0.715572] . ( 0 sec) [ -3205.9405] [Topology ] . ( 1 sec) [ -3185.8438] [Topology ] . ( 1 sec) [ -3182.6057] [Topology ] . ( 2 sec) [ -3180.8613] [Topology ] . ( 2 sec) [ -3180.4036] [Topology ] . ( 3 sec) [ -3180.3247] [Topology ] . ( 4 sec) [ -3180.2902] [Topology ] . ( 4 sec) [ -3180.2719] [Topology ] . ( 5 sec) [ -3180.2615] [Topology ] . ( 5 sec) [ -3180.2554] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -3179.9529] [Alpha ][ 0.791776] . ( 9 sec) [ -3179.9529] [Topology ] . ( 10 sec) [ -3179.9261] [Topology ] . ( 10 sec) [ -3179.9145] [Topology ] . ( 11 sec) [ -3179.9081] [Topology ] . ( 12 sec) [ -3179.9046] [Topology ] . ( 12 sec) [ -3179.9026] [Topology ] . ( 13 sec) [ -3179.9014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -3179.8991] [Alpha ][ 0.798974] . ( 17 sec) [ -3179.8991] [Topology ] . ( 17 sec) [ -3179.8981] [Topology ] . ( 18 sec) [ -3179.8975] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -3179.8975] [Alpha ][ 0.799773] . ( 22 sec) [ -3179.8975] [Topology ] . ( 23 sec) [ -3179.8971] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 31 sec) [ -3205.9405] [Alpha ][ 0.715572] . ( 31 sec) [ -3204.8230] [ 588] [depth= 1] . ( 31 sec) [ -3204.4975] [ 588] [depth= 1] . ( 32 sec) [ -3202.1815] [ 588] [depth= 1] . ( 32 sec) [ -3201.6828] [ 588] [depth= 1] . ( 32 sec) [ -3201.4585] [ 588] [depth= 1] . ( 32 sec) [ -3201.3209] [ 588] [depth= 1] . ( 33 sec) [ -3200.3034] [ 590] [depth= 1] . ( 33 sec) [ -3196.8229] [ 588] [depth= 1] . ( 34 sec) [ -3194.9065] [ 588] [depth= 1] . ( 36 sec) [ -3194.8109] [ 590] [depth= 1] . ( 36 sec) [ -3194.0856] [ 588] [depth= 1] . ( 36 sec) [ -3192.5816] [ 587] [depth= 1] . ( 36 sec) [ -3188.0278] [ 586] [depth= 2] . ( 38 sec) [ -3187.7771] [ 587] [depth= 1] . ( 39 sec) [ -3181.9854] [Branch lengths ] . ( 39 sec) [ -3181.8290] [Alpha ][ 0.769967] . ( 41 sec) [ -3181.0234] [ 587] [depth= 1] . ( 48 sec) [ -3180.0617] [Branch lengths ] . ( 49 sec) [ -3180.0407] [Alpha ][ 0.790686] . ( 58 sec) [ -3179.9257] [Branch lengths ] . ( 58 sec) [ -3179.9257] [Topology ] . ( 59 sec) [ -3179.9121] [Topology ] . ( 59 sec) [ -3179.9069] [Topology ] . ( 60 sec) [ -3179.9042] [Topology ] . ( 60 sec) [ -3179.9027] [Topology ] . ( 61 sec) [ -3179.9018] [Topology ] . ( 61 sec) [ -3179.8986] [Alpha ][ 0.799119] . ( 61 sec) [ -3179.8986] [Topology ] . ( 62 sec) [ -3179.8978] [Topology ] . ( 62 sec) [ -3179.8978] [Alpha ][ 0.799119] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3179.897122 . Log likelihood obtained after SPR moves : -3179.897758 . Log likelihood of the current tree: -3179.897122. . Printing the most likely tree in file 'proteic_M1989_18x173_2004.phy_phyml_tree.txt'... . Best log likelihood : -3179.897113 . Time used 0h1m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 249.06user 0.00system 4:13.21elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps