.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2512_14x717_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... . 703 patterns found. (out of a total of 717 sites) . 39 sites without polymorphism (5.44%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -33335.8655] [Alpha ][ 0.500960] . ( 2 sec) [ -24851.4018] [ 4710] [depth= 3] . ( 2 sec) [ -23755.0930] [ 4689] [depth= 3] . ( 3 sec) [ -23742.6210] [ 4690] [depth= 1] . ( 3 sec) [ -22755.7667] [ 4660] [depth= 3] . ( 3 sec) [ -22385.2432] [ 4623] [depth= 2] . ( 4 sec) [ -22259.7613] [ 4601] [depth= 2] . ( 4 sec) [ -22254.5270] [ 4612] [depth= 1] . ( 5 sec) [ -22221.3291] [ 4640] [depth= 1] . ( 5 sec) [ -22220.5686] [ 4639] [depth= 1] . ( 5 sec) [ -22138.5419] [ 4626] [depth= 1] . ( 6 sec) [ -21937.6799] [ 4584] [depth= 1] . ( 6 sec) [ -21863.4943] [ 4593] [depth= 2] . ( 7 sec) [ -21666.4896] [ 4578] [depth= 2] . ( 7 sec) [ -21601.0401] [ 4584] [depth= 1] . ( 7 sec) [ -21589.8547] [ 4585] [depth= 1] . ( 8 sec) [ -21554.2443] [ 4590] [depth= 1] . ( 9 sec) [ -21306.0347] [ 4584] [depth= 1] . ( 10 sec) [ -21298.5169] [ 4580] [depth= 3] . ( 11 sec) [ -21246.9638] [ 4582] [depth= 2] . ( 11 sec) [ -21142.7799] [ 4589] [depth= 2] . ( 11 sec) [ -21130.7818] [ 4589] [depth= 2] . ( 12 sec) [ -21126.8850] [ 4593] [depth= 1] . ( 13 sec) [ -20963.6070] [ 4557] [depth= 3] . ( 13 sec) [ -20959.9794] [ 4538] [depth= 2] . ( 13 sec) [ -20950.8961] [ 4540] [depth= 1] . ( 14 sec) [ -20727.9336] [ 4530] [depth= 1] . ( 15 sec) [ -20227.0759] [Branch lengths ] . ( 15 sec) [ -20182.7191] [Alpha ][ 0.774738] . ( 16 sec) [ -20159.2204] [ 4533] [depth= 1] . ( 16 sec) [ -20157.8180] [ 4539] [depth= 1] . ( 17 sec) [ -20157.2034] [ 4533] [depth= 1] . ( 18 sec) [ -20154.7568] [ 4525] [depth= 2] . ( 19 sec) [ -20146.6436] [ 4519] [depth= 2] . ( 20 sec) [ -20145.7698] [ 4516] [depth= 1] . ( 22 sec) [ -20144.9447] [ 4512] [depth= 1] . ( 24 sec) [ -20144.2240] [ 4513] [depth= 1] . ( 25 sec) [ -20126.9157] [Branch lengths ] . ( 25 sec) [ -20123.6482] [Alpha ][ 0.867961] . ( 28 sec) [ -20123.4915] [ 4517] [depth= 1] . ( 36 sec) [ -20122.3216] [ 4518] [depth= 1] . ( 37 sec) [ -20115.9782] [Branch lengths ] . ( 37 sec) [ -20114.2473] [Alpha ][ 0.946114] . ( 45 sec) [ -20113.9423] [ 4519] [depth= 1] . ( 48 sec) [ -20113.5743] [ 4524] [depth= 1] . ( 49 sec) [ -20108.9114] [Branch lengths ] . ( 49 sec) [ -20108.1766] [Alpha ][ 1.002369] . ( 62 sec) [ -20107.9418] [ 4519] [depth= 1] . ( 63 sec) [ -20105.3850] [Branch lengths ] . ( 63 sec) [ -20104.6168] [Alpha ][ 1.066256] . ( 75 sec) [ -20104.3449] [ 4524] [depth= 1] . ( 76 sec) [ -20102.7927] [Branch lengths ] . ( 76 sec) [ -20102.4809] [Alpha ][ 1.110339] . ( 89 sec) [ -20102.4523] [ 4519] [depth= 1] . ( 89 sec) [ -20101.5571] [Branch lengths ] . ( 90 sec) [ -20101.3175] [Alpha ][ 1.150986] . ( 102 sec) [ -20101.2131] [ 4524] [depth= 1] . ( 103 sec) [ -20100.7518] [Branch lengths ] . ( 103 sec) [ -20100.6626] [Alpha ][ 1.177391] . ( 103 sec) [ -20100.6626] [Topology ] . ( 105 sec) [ -20100.4603] [Topology ] . ( 107 sec) [ -20100.3699] [Topology ] . ( 109 sec) [ -20100.3140] [Topology ] . ( 111 sec) [ -20100.2748] [Topology ] . ( 113 sec) [ -20100.2449] [Topology ] . ( 115 sec) [ -20100.2215] [Topology ] . ( 115 sec) [ -20100.1201] [Alpha ][ 1.206676] . ( 115 sec) [ -20100.1201] [Topology ] . ( 117 sec) [ -20100.0514] [Topology ] . ( 119 sec) [ -20100.0201] [Topology ] . ( 121 sec) [ -20099.9995] [Topology ] . ( 123 sec) [ -20099.9843] [Topology ] . ( 125 sec) [ -20099.9724] [Topology ] . ( 127 sec) [ -20099.9627] [Topology ] . ( 127 sec) [ -20099.9270] [Alpha ][ 1.224527] . ( 127 sec) [ -20099.9270] [Topology ] . ( 129 sec) [ -20099.9016] [Topology ] . ( 131 sec) [ -20099.8896] [Topology ] . ( 133 sec) [ -20099.8813] [Topology ] . ( 135 sec) [ -20099.8750] [Topology ] . ( 137 sec) [ -20099.8699] [Topology ] . ( 139 sec) [ -20099.8656] [Topology ] . ( 139 sec) [ -20099.8534] [Alpha ][ 1.235098] . ( 139 sec) [ -20099.8534] [Topology ] . ( 141 sec) [ -20099.8440] [Topology ] . ( 143 sec) [ -20099.8391] [Topology ] . ( 145 sec) [ -20099.8356] [Topology ] . ( 147 sec) [ -20099.8328] [Topology ] . ( 149 sec) [ -20099.8305] [Topology ] . ( 151 sec) [ -20099.8285] [Topology ] . ( 151 sec) [ -20099.8244] [Alpha ][ 1.241226] . ( 151 sec) [ -20099.8244] [Topology ] . ( 153 sec) [ -20099.8208] [Topology ] . ( 155 sec) [ -20099.8187] [Topology ] . ( 157 sec) [ -20099.8172] [Topology ] . ( 159 sec) [ -20099.8159] [Topology ] . ( 161 sec) [ -20099.8148] [Topology ] . ( 163 sec) [ -20099.8139] [Topology ] . ( 163 sec) [ -20099.8125] [Alpha ][ 1.244739] . ( 163 sec) [ -20099.8125] [Topology ] . ( 165 sec) [ -20099.8111] [Topology ] . ( 167 sec) [ -20099.8102] [Topology ] . ( 168 sec) [ -20099.8100] [Alpha ][ 1.246128] . ( 168 sec) [ -20099.8100] [Topology ] . ( 170 sec) [ -20099.8091] [Topology ] . ( 170 sec) [ -20099.8089] [Alpha ][ 1.247374] . ( 170 sec) [ -20099.8089] [Topology ] . ( 172 sec) [ -20099.8081] [Topology ] . ( 172 sec) [ -20099.8081] [Alpha ][ 1.247374] . Checking for NNIs, optimizing five branches... . ( 203 sec) [ -20099.7250] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20099.725011. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -25214.5920] [Alpha ][ 0.500960] . ( 1 sec) [ -24509.9091] [ 5088] [depth= 1] . ( 1 sec) [ -23913.7387] [ 5061] [depth= 4] . ( 2 sec) [ -23712.8682] [ 5002] [depth= 2] . ( 2 sec) [ -23302.7588] [ 4929] [depth= 3] . ( 3 sec) [ -22720.8034] [ 4831] [depth= 2] . ( 3 sec) [ -22001.8515] [ 4786] [depth= 1] . ( 4 sec) [ -21893.5035] [ 4790] [depth= 1] . ( 4 sec) [ -21728.1708] [ 4626] [depth= 3] . ( 5 sec) [ -21721.8470] [ 4609] [depth= 5] . ( 5 sec) [ -21550.1697] [ 4599] [depth= 1] . ( 5 sec) [ -21499.7904] [ 4601] [depth= 1] . ( 6 sec) [ -21369.4207] [ 4594] [depth= 2] . ( 6 sec) [ -21192.3411] [ 4602] [depth= 2] . ( 7 sec) [ -21065.9074] [ 4593] [depth= 1] . ( 7 sec) [ -20840.8805] [ 4561] [depth= 1] . ( 7 sec) [ -20649.1522] [ 4591] [depth= 2] . ( 8 sec) [ -20632.7721] [ 4623] [depth= 1] . ( 8 sec) [ -20626.5556] [ 4606] [depth= 2] . ( 9 sec) [ -20588.5354] [ 4605] [depth= 1] . ( 9 sec) [ -20481.0913] [ 4612] [depth= 1] . ( 10 sec) [ -20476.0508] [ 4617] [depth= 1] . ( 10 sec) [ -20458.0198] [ 4581] [depth= 1] . ( 11 sec) [ -20409.5164] [ 4538] [depth= 3] . ( 11 sec) [ -20399.8391] [ 4538] [depth= 1] . ( 12 sec) [ -20392.5874] [ 4592] [depth= 1] . ( 13 sec) [ -20390.4297] [ 4593] [depth= 1] . ( 13 sec) [ -20202.0946] [Branch lengths ] . ( 14 sec) [ -20125.5097] [Alpha ][ 0.999969] . ( 15 sec) [ -20123.7135] [ 4602] [depth= 2] . ( 16 sec) [ -20122.3436] [ 4588] [depth= 2] . ( 17 sec) [ -20121.3248] [ 4588] [depth= 1] . ( 19 sec) [ -20120.5460] [ 4516] [depth= 4] . ( 22 sec) [ -20119.4950] [ 4519] [depth= 1] . ( 23 sec) [ -20117.3808] [ 4516] [depth= 1] . ( 24 sec) [ -20105.9361] [Branch lengths ] . ( 24 sec) [ -20102.4153] [Alpha ][ 1.152407] . ( 34 sec) [ -20100.6288] [Branch lengths ] . ( 34 sec) [ -20100.6288] [Topology ] . ( 36 sec) [ -20100.4749] [Topology ] . ( 37 sec) [ -20100.4032] [Topology ] . ( 39 sec) [ -20100.3616] [Topology ] . ( 41 sec) [ -20100.3343] [Topology ] . ( 43 sec) [ -20100.3158] [Topology ] . ( 45 sec) [ -20100.3030] [Topology ] . ( 45 sec) [ -20100.0443] [Alpha ][ 1.197286] . ( 46 sec) [ -20100.0443] [Topology ] . ( 48 sec) [ -20099.9455] [Topology ] . ( 49 sec) [ -20099.9147] [Topology ] . ( 51 sec) [ -20099.9008] [Topology ] . ( 53 sec) [ -20099.8933] [Topology ] . ( 55 sec) [ -20099.8890] [Topology ] . ( 57 sec) [ -20099.8863] [Topology ] . ( 57 sec) [ -20099.8243] [Alpha ][ 1.220688] . ( 58 sec) [ -20099.8243] [Topology ] . ( 59 sec) [ -20099.7962] [Topology ] . ( 61 sec) [ -20099.7869] [Topology ] . ( 63 sec) [ -20099.7827] [Topology ] . ( 65 sec) [ -20099.7805] [Topology ] . ( 67 sec) [ -20099.7792] [Topology ] . ( 69 sec) [ -20099.7785] [Topology ] . ( 69 sec) [ -20099.7610] [Alpha ][ 1.233343] . ( 70 sec) [ -20099.7610] [Topology ] . ( 71 sec) [ -20099.7528] [Topology ] . ( 73 sec) [ -20099.7501] [Topology ] . ( 75 sec) [ -20099.7489] [Topology ] . ( 77 sec) [ -20099.7482] [Topology ] . ( 78 sec) [ -20099.7439] [Alpha ][ 1.239661] . ( 78 sec) [ -20099.7439] [Topology ] . ( 80 sec) [ -20099.7411] [Topology ] . ( 81 sec) [ -20099.7400] [Topology ] . ( 83 sec) [ -20099.7395] [Topology ] . ( 84 sec) [ -20099.7374] [Alpha ][ 1.244042] . ( 84 sec) [ -20099.7374] [Topology ] . ( 86 sec) [ -20099.7362] [Topology ] . ( 88 sec) [ -20099.7359] [Topology ] . ( 88 sec) [ -20099.7355] [Alpha ][ 1.245669] . ( 88 sec) [ -20099.7355] [Topology ] . ( 90 sec) [ -20099.7351] [Topology ] . ( 90 sec) [ -20099.7350] [Alpha ][ 1.246915] . Checking for NNIs, optimizing five branches... . ( 120 sec) [ -20099.6603] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20099.660257. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24676.1192] [Alpha ][ 0.500960] . ( 2 sec) [ -24343.5149] [ 4845] [depth= 6] . ( 2 sec) [ -24313.5045] [ 4822] [depth= 4] . ( 3 sec) [ -24262.9383] [ 4822] [depth= 3] . ( 3 sec) [ -23178.2679] [ 4787] [depth= 1] . ( 3 sec) [ -23004.2652] [ 4741] [depth= 1] . ( 4 sec) [ -21168.7133] [ 4588] [depth= 2] . ( 4 sec) [ -21168.6931] [ 4581] [depth= 1] . ( 4 sec) [ -20908.7392] [ 4586] [depth= 1] . ( 5 sec) [ -20821.3344] [ 4563] [depth= 1] . ( 6 sec) [ -20800.7720] [ 4551] [depth= 2] . ( 6 sec) [ -20647.2742] [ 4538] [depth= 1] . ( 7 sec) [ -20540.7291] [ 4533] [depth= 2] . ( 7 sec) [ -20537.6876] [ 4536] [depth= 2] . ( 8 sec) [ -20533.2594] [ 4538] [depth= 2] . ( 9 sec) [ -20526.3804] [ 4533] [depth= 1] . ( 9 sec) [ -20518.5663] [ 4545] [depth= 1] . ( 9 sec) [ -20517.7251] [ 4534] [depth= 2] . ( 10 sec) [ -20466.8265] [ 4528] [depth= 1] . ( 10 sec) [ -20437.5928] [ 4534] [depth= 1] . ( 11 sec) [ -20403.8480] [ 4528] [depth= 1] . ( 13 sec) [ -20235.6573] [Branch lengths ] . ( 14 sec) [ -20152.7613] [Alpha ][ 1.000909] . ( 14 sec) [ -20138.5055] [ 4532] [depth= 1] . ( 15 sec) [ -20134.0408] [ 4528] [depth= 1] . ( 16 sec) [ -20131.0844] [ 4536] [depth= 1] . ( 18 sec) [ -20130.8050] [ 4536] [depth= 1] . ( 22 sec) [ -20128.6309] [ 4526] [depth= 1] . ( 22 sec) [ -20127.2698] [ 4516] [depth= 1] . ( 23 sec) [ -20126.8647] [ 4528] [depth= 1] . ( 23 sec) [ -20126.8010] [ 4532] [depth= 1] . ( 26 sec) [ -20113.7752] [Branch lengths ] . ( 27 sec) [ -20110.5744] [Alpha ][ 1.147858] . ( 34 sec) [ -20106.2901] [ 4532] [depth= 2] . ( 38 sec) [ -20105.8189] [ 4532] [depth= 1] . ( 42 sec) [ -20102.2857] [Branch lengths ] . ( 42 sec) [ -20102.0699] [Alpha ][ 1.189252] . ( 58 sec) [ -20101.9199] [ 4532] [depth= 1] . ( 61 sec) [ -20099.2715] [Branch lengths ] . ( 61 sec) [ -20099.2207] [Alpha ][ 1.210300] . ( 78 sec) [ -20098.6397] [Branch lengths ] . ( 78 sec) [ -20098.6397] [Topology ] . ( 80 sec) [ -20098.5468] [Topology ] . ( 82 sec) [ -20098.4952] [Topology ] . ( 84 sec) [ -20098.4611] [Topology ] . ( 86 sec) [ -20098.4365] [Topology ] . ( 88 sec) [ -20098.4182] [Topology ] . ( 90 sec) [ -20098.4045] [Topology ] . ( 90 sec) [ -20098.3546] [Alpha ][ 1.231715] . ( 91 sec) [ -20098.3546] [Topology ] . ( 93 sec) [ -20098.3247] [Topology ] . ( 95 sec) [ -20098.3120] [Topology ] . ( 97 sec) [ -20098.3040] [Topology ] . ( 99 sec) [ -20098.2982] [Topology ] . ( 100 sec) [ -20098.2938] [Topology ] . ( 102 sec) [ -20098.2903] [Topology ] . ( 103 sec) [ -20098.2787] [Alpha ][ 1.242168] . ( 103 sec) [ -20098.2787] [Topology ] . ( 105 sec) [ -20098.2709] [Topology ] . ( 107 sec) [ -20098.2672] [Topology ] . ( 109 sec) [ -20098.2647] [Topology ] . ( 111 sec) [ -20098.2627] [Topology ] . ( 113 sec) [ -20098.2612] [Topology ] . ( 115 sec) [ -20098.2598] [Topology ] . ( 115 sec) [ -20098.2566] [Alpha ][ 1.247653] . ( 115 sec) [ -20098.2566] [Topology ] . ( 117 sec) [ -20098.2541] [Topology ] . ( 119 sec) [ -20098.2527] [Topology ] . ( 121 sec) [ -20098.2516] [Topology ] . ( 123 sec) [ -20098.2508] [Topology ] . ( 124 sec) [ -20098.2500] [Alpha ][ 1.250332] . ( 124 sec) [ -20098.2500] [Topology ] . ( 126 sec) [ -20098.2489] [Topology ] . ( 128 sec) [ -20098.2481] [Topology ] . ( 128 sec) [ -20098.2479] [Alpha ][ 1.251582] . ( 128 sec) [ -20098.2479] [Topology ] . ( 130 sec) [ -20098.2471] [Topology ] . ( 131 sec) [ -20098.2470] [Alpha ][ 1.252834] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20098.247050. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24019.1644] [Alpha ][ 0.500960] . ( 1 sec) [ -23309.0394] [ 5050] [depth= 6] . ( 1 sec) [ -22997.0496] [ 5025] [depth= 2] . ( 2 sec) [ -22975.6965] [ 4959] [depth= 4] . ( 2 sec) [ -22950.6586] [ 4954] [depth= 1] . ( 3 sec) [ -22946.0655] [ 4958] [depth= 1] . ( 3 sec) [ -22819.7007] [ 4869] [depth= 2] . ( 3 sec) [ -22653.9369] [ 4743] [depth= 1] . ( 4 sec) [ -22364.1586] [ 4731] [depth= 5] . ( 4 sec) [ -22230.6450] [ 4745] [depth= 1] . ( 4 sec) [ -21802.9457] [ 4695] [depth= 4] . ( 5 sec) [ -21742.7902] [ 4700] [depth= 1] . ( 6 sec) [ -21732.4531] [ 4701] [depth= 1] . ( 6 sec) [ -21719.5937] [ 4688] [depth= 1] . ( 6 sec) [ -21714.8533] [ 4693] [depth= 2] . ( 7 sec) [ -21499.3217] [ 4676] [depth= 6] . ( 7 sec) [ -21435.7437] [ 4658] [depth= 3] . ( 8 sec) [ -21383.0818] [ 4631] [depth= 2] . ( 8 sec) [ -21374.8278] [ 4629] [depth= 1] . ( 9 sec) [ -21297.3701] [ 4624] [depth= 2] . ( 9 sec) [ -21262.2901] [ 4626] [depth= 1] . ( 10 sec) [ -20840.6486] [ 4617] [depth= 2] . ( 10 sec) [ -20837.2119] [ 4579] [depth= 3] . ( 10 sec) [ -20779.5322] [ 4550] [depth= 4] . ( 11 sec) [ -20765.4763] [ 4545] [depth= 1] . ( 11 sec) [ -20753.5215] [ 4677] [depth= 1] . ( 12 sec) [ -20744.0685] [ 4661] [depth= 2] . ( 12 sec) [ -20360.1105] [ 4542] [depth= 1] . ( 13 sec) [ -20327.5033] [ 4530] [depth= 1] . ( 14 sec) [ -20242.7327] [Branch lengths ] . ( 14 sec) [ -20206.4905] [Alpha ][ 0.748760] . ( 16 sec) [ -20188.2382] [ 4528] [depth= 1] . ( 17 sec) [ -20185.8499] [ 4533] [depth= 1] . ( 18 sec) [ -20184.0000] [ 4522] [depth= 3] . ( 20 sec) [ -20181.0639] [ 4512] [depth= 1] . ( 21 sec) [ -20177.9466] [ 4525] [depth= 2] . ( 23 sec) [ -20156.7644] [ 4529] [depth= 1] . ( 23 sec) [ -20152.2763] [ 4532] [depth= 1] . ( 24 sec) [ -20151.4641] [ 4519] [depth= 4] . ( 25 sec) [ -20125.7281] [Branch lengths ] . ( 25 sec) [ -20116.2453] [Alpha ][ 0.925552] . ( 34 sec) [ -20115.8045] [ 4517] [depth= 1] . ( 37 sec) [ -20114.5927] [ 4518] [depth= 1] . ( 38 sec) [ -20109.4730] [Branch lengths ] . ( 38 sec) [ -20107.3535] [Alpha ][ 1.024299] . ( 46 sec) [ -20107.2537] [ 4519] [depth= 1] . ( 49 sec) [ -20107.2224] [ 4519] [depth= 1] . ( 50 sec) [ -20105.0414] [Branch lengths ] . ( 50 sec) [ -20104.1242] [Alpha ][ 1.097090] . ( 63 sec) [ -20103.3882] [ 4519] [depth= 1] . ( 64 sec) [ -20102.0430] [Branch lengths ] . ( 64 sec) [ -20101.7887] [Alpha ][ 1.138113] . ( 77 sec) [ -20101.0459] [Branch lengths ] . ( 77 sec) [ -20101.0459] [Topology ] . ( 79 sec) [ -20100.9037] [Topology ] . ( 81 sec) [ -20100.8253] [Topology ] . ( 83 sec) [ -20100.7723] [Topology ] . ( 84 sec) [ -20100.7329] [Topology ] . ( 86 sec) [ -20100.7029] [Topology ] . ( 88 sec) [ -20100.6795] [Topology ] . ( 89 sec) [ -20100.3725] [Alpha ][ 1.187045] . ( 89 sec) [ -20100.3725] [Topology ] . ( 91 sec) [ -20100.2376] [Topology ] . ( 93 sec) [ -20100.1882] [Topology ] . ( 94 sec) [ -20100.1613] [Topology ] . ( 96 sec) [ -20100.1443] [Topology ] . ( 98 sec) [ -20100.1326] [Topology ] . ( 100 sec) [ -20100.1243] [Topology ] . ( 100 sec) [ -20100.0442] [Alpha ][ 1.213396] . ( 101 sec) [ -20100.0442] [Topology ] . ( 103 sec) [ -20100.0022] [Topology ] . ( 104 sec) [ -20099.9856] [Topology ] . ( 106 sec) [ -20099.9764] [Topology ] . ( 108 sec) [ -20099.9705] [Topology ] . ( 110 sec) [ -20099.9664] [Topology ] . ( 112 sec) [ -20099.9635] [Topology ] . ( 112 sec) [ -20099.9387] [Alpha ][ 1.228376] . ( 113 sec) [ -20099.9387] [Topology ] . ( 114 sec) [ -20099.9251] [Topology ] . ( 116 sec) [ -20099.9196] [Topology ] . ( 118 sec) [ -20099.9164] [Topology ] . ( 120 sec) [ -20099.9143] [Topology ] . ( 122 sec) [ -20099.9128] [Topology ] . ( 124 sec) [ -20099.9116] [Topology ] . ( 124 sec) [ -20099.9036] [Alpha ][ 1.236952] . ( 124 sec) [ -20099.9036] [Topology ] . ( 126 sec) [ -20099.8991] [Topology ] . ( 128 sec) [ -20099.8971] [Topology ] . ( 130 sec) [ -20099.8959] [Topology ] . ( 132 sec) [ -20099.8951] [Topology ] . ( 132 sec) [ -20099.8929] [Alpha ][ 1.241373] . ( 132 sec) [ -20099.8929] [Topology ] . ( 134 sec) [ -20099.8911] [Topology ] . ( 136 sec) [ -20099.8901] [Topology ] . ( 137 sec) [ -20099.8897] [Alpha ][ 1.243367] . ( 137 sec) [ -20099.8897] [Topology ] . ( 139 sec) [ -20099.8886] [Topology ] . ( 141 sec) [ -20099.8880] [Topology ] . ( 141 sec) [ -20099.8877] [Alpha ][ 1.244736] . ( 141 sec) [ -20099.8877] [Topology ] . ( 143 sec) [ -20099.8871] [Topology ] . ( 143 sec) [ -20099.8868] [Alpha ][ 1.246113] . Checking for NNIs, optimizing five branches... . ( 169 sec) [ -20099.8015] [Topology ] . Checking for NNIs, optimizing five branches... . ( 197 sec) [ -20099.7257] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20099.725677. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26668.9452] [Alpha ][ 0.500960] . ( 1 sec) [ -26392.9244] [ 5103] [depth= 5] . ( 2 sec) [ -26288.0998] [ 5054] [depth= 6] . ( 2 sec) [ -26265.0459] [ 5038] [depth= 1] . ( 3 sec) [ -25787.7234] [ 4984] [depth= 2] . ( 3 sec) [ -25607.7165] [ 4871] [depth= 3] . ( 3 sec) [ -25364.3856] [ 4876] [depth= 4] . ( 4 sec) [ -23899.9831] [ 4862] [depth= 1] . ( 5 sec) [ -23454.1562] [ 4859] [depth= 1] . ( 6 sec) [ -23002.1089] [ 4808] [depth= 3] . ( 6 sec) [ -22957.9411] [ 4791] [depth= 2] . ( 6 sec) [ -22782.0286] [ 4793] [depth= 1] . ( 7 sec) [ -22744.2689] [ 4776] [depth= 5] . ( 7 sec) [ -22116.1532] [ 4767] [depth= 5] . ( 8 sec) [ -21765.0240] [ 4624] [depth= 1] . ( 8 sec) [ -21671.7009] [ 4621] [depth= 1] . ( 8 sec) [ -21308.6988] [ 4618] [depth= 2] . ( 9 sec) [ -21306.4026] [ 4616] [depth= 1] . ( 9 sec) [ -21219.2109] [ 4593] [depth= 2] . ( 10 sec) [ -21119.1193] [ 4583] [depth= 1] . ( 10 sec) [ -21115.9854] [ 4581] [depth= 2] . ( 11 sec) [ -21068.3080] [ 4540] [depth= 2] . ( 11 sec) [ -21059.8349] [ 4531] [depth= 1] . ( 12 sec) [ -21041.6958] [ 4536] [depth= 2] . ( 12 sec) [ -20986.5915] [ 4550] [depth= 1] . ( 13 sec) [ -20977.6646] [ 4556] [depth= 1] . ( 13 sec) [ -20962.7956] [ 4552] [depth= 1] . ( 14 sec) [ -20239.9418] [Branch lengths ] . ( 15 sec) [ -20185.0129] [Alpha ][ 0.919209] . ( 15 sec) [ -20169.6527] [ 4539] [depth= 1] . ( 16 sec) [ -20168.2018] [ 4543] [depth= 1] . ( 17 sec) [ -20165.6280] [ 4538] [depth= 1] . ( 17 sec) [ -20164.3091] [ 4543] [depth= 1] . ( 19 sec) [ -20149.3500] [ 4543] [depth= 2] . ( 19 sec) [ -20145.5134] [ 4527] [depth= 2] . ( 20 sec) [ -20140.7108] [ 4536] [depth= 1] . ( 27 sec) [ -20137.8979] [ 4536] [depth= 1] . ( 28 sec) [ -20122.6144] [Branch lengths ] . ( 28 sec) [ -20120.7019] [Alpha ][ 1.017881] . ( 30 sec) [ -20119.7368] [ 4539] [depth= 1] . ( 35 sec) [ -20118.0997] [ 4529] [depth= 1] . ( 45 sec) [ -20109.7027] [Branch lengths ] . ( 45 sec) [ -20108.4551] [Alpha ][ 1.105567] . ( 53 sec) [ -20107.6728] [ 4532] [depth= 1] . ( 64 sec) [ -20105.0983] [Branch lengths ] . ( 64 sec) [ -20104.7078] [Alpha ][ 1.158430] . ( 72 sec) [ -20104.5494] [ 4532] [depth= 1] . ( 81 sec) [ -20101.8562] [Branch lengths ] . ( 82 sec) [ -20101.7351] [Alpha ][ 1.188808] . ( 99 sec) [ -20099.3671] [Branch lengths ] . ( 99 sec) [ -20099.3671] [Topology ] . ( 101 sec) [ -20099.0581] [Topology ] . ( 103 sec) [ -20098.8922] [Topology ] . ( 105 sec) [ -20098.7843] [Topology ] . ( 107 sec) [ -20098.7092] [Topology ] . ( 109 sec) [ -20098.6553] [Topology ] . ( 111 sec) [ -20098.6160] [Topology ] . ( 111 sec) [ -20098.4961] [Alpha ][ 1.220252] . ( 111 sec) [ -20098.4961] [Topology ] . ( 113 sec) [ -20098.4248] [Topology ] . ( 115 sec) [ -20098.3932] [Topology ] . ( 117 sec) [ -20098.3734] [Topology ] . ( 119 sec) [ -20098.3595] [Topology ] . ( 121 sec) [ -20098.3493] [Topology ] . ( 123 sec) [ -20098.3415] [Topology ] . ( 123 sec) [ -20098.3128] [Alpha ][ 1.236592] . ( 123 sec) [ -20098.3128] [Topology ] . ( 125 sec) [ -20098.2947] [Topology ] . ( 127 sec) [ -20098.2869] [Topology ] . ( 129 sec) [ -20098.2819] [Topology ] . ( 131 sec) [ -20098.2783] [Topology ] . ( 133 sec) [ -20098.2755] [Topology ] . ( 135 sec) [ -20098.2732] [Topology ] . ( 136 sec) [ -20098.2659] [Alpha ][ 1.244907] . ( 136 sec) [ -20098.2659] [Topology ] . ( 138 sec) [ -20098.2609] [Topology ] . ( 140 sec) [ -20098.2585] [Topology ] . ( 142 sec) [ -20098.2568] [Topology ] . ( 144 sec) [ -20098.2555] [Topology ] . ( 146 sec) [ -20098.2545] [Topology ] . ( 148 sec) [ -20098.2535] [Topology ] . ( 148 sec) [ -20098.2516] [Alpha ][ 1.249193] . ( 148 sec) [ -20098.2516] [Topology ] . ( 150 sec) [ -20098.2499] [Topology ] . ( 152 sec) [ -20098.2490] [Topology ] . ( 152 sec) [ -20098.2487] [Alpha ][ 1.250826] . ( 153 sec) [ -20098.2487] [Topology ] . ( 155 sec) [ -20098.2477] [Topology ] . ( 155 sec) [ -20098.2476] [Alpha ][ 1.252077] . ( 155 sec) [ -20098.2476] [Topology ] . ( 157 sec) [ -20098.2468] [Topology ] . ( 157 sec) [ -20098.2468] [Alpha ][ 1.252077] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20098.246766. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -20898.1075] [Alpha ][ 1.719622] . ( 1 sec) [ -20898.1075] [Topology ] . ( 2 sec) [ -20323.7506] [Topology ] . ( 4 sec) [ -20209.4899] [Topology ] . ( 6 sec) [ -20190.1580] [Topology ] . ( 7 sec) [ -20183.4133] [Topology ] . ( 9 sec) [ -20179.6054] [Topology ] . ( 10 sec) [ -20178.2734] [Topology ] . ( 12 sec) [ -20177.5990] [Topology ] . ( 14 sec) [ -20177.2069] [Topology ] . ( 15 sec) [ -20176.9503] [Topology ] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -20111.7538] [Topology ] . ( 52 sec) [ -20108.0232] [Alpha ][ 1.456524] . ( 53 sec) [ -20108.0232] [Topology ] . ( 54 sec) [ -20106.2903] [Topology ] . ( 56 sec) [ -20105.8153] [Topology ] . ( 58 sec) [ -20105.6133] [Topology ] . ( 60 sec) [ -20105.5047] [Topology ] . ( 62 sec) [ -20105.4368] [Topology ] . ( 64 sec) [ -20105.3898] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -20104.4147] [Topology ] . ( 87 sec) [ -20103.4762] [Alpha ][ 1.346223] . ( 87 sec) [ -20103.4762] [Topology ] . ( 89 sec) [ -20103.0390] [Topology ] . ( 91 sec) [ -20102.9113] [Topology ] . ( 93 sec) [ -20102.8527] [Topology ] . ( 95 sec) [ -20102.8185] [Topology ] . ( 97 sec) [ -20102.7957] [Topology ] . ( 98 sec) [ -20102.7794] [Topology ] . Checking for NNIs, optimizing five branches... . ( 126 sec) [ -20102.5334] [Alpha ][ 1.294348] . ( 127 sec) [ -20102.5334] [Topology ] . ( 128 sec) [ -20102.4148] [Topology ] . ( 130 sec) [ -20102.3768] [Topology ] . ( 132 sec) [ -20102.3577] [Topology ] . ( 134 sec) [ -20102.3458] [Topology ] . ( 136 sec) [ -20102.3377] [Topology ] . ( 138 sec) [ -20102.3318] [Topology ] . Checking for NNIs, optimizing five branches... . ( 165 sec) [ -20102.2632] [Alpha ][ 1.268600] . ( 166 sec) [ -20102.2632] [Topology ] . ( 167 sec) [ -20102.2296] [Topology ] . ( 169 sec) [ -20102.2181] [Topology ] . ( 171 sec) [ -20102.2122] [Topology ] . ( 173 sec) [ -20102.2084] [Topology ] . ( 175 sec) [ -20102.2060] [Topology ] . ( 177 sec) [ -20102.2042] [Topology ] . Checking for NNIs, optimizing five branches... . ( 204 sec) [ -20102.1834] [Alpha ][ 1.254001] . ( 204 sec) [ -20102.1834] [Topology ] . ( 206 sec) [ -20102.1724] [Topology ] . ( 208 sec) [ -20102.1689] [Topology ] . ( 210 sec) [ -20102.1673] [Topology ] . ( 212 sec) [ -20102.1665] [Topology ] . Checking for NNIs, optimizing five branches... . ( 240 sec) [ -20102.1615] [Alpha ][ 1.246927] . ( 240 sec) [ -20102.1615] [Topology ] . ( 242 sec) [ -20102.1586] [Topology ] . ( 244 sec) [ -20102.1579] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -20102.1571] [Alpha ][ 1.243876] . ( 272 sec) [ -20102.1571] [Topology ] . ( 273 sec) [ -20102.1565] [Topology ] . Checking for NNIs, optimizing five branches... . ( 300 sec) [ -20102.1551] [Alpha ][ 1.240063] . ( 300 sec) [ -20102.1551] [Topology ] . ( 302 sec) [ -20102.1540] [Topology ] . ( 304 sec) [ -20102.1546] [Topology ] . Checking for NNIs, optimizing five branches... . ( 330 sec) [ -20102.1541] [Alpha ][ 1.237895] . ( 330 sec) [ -20102.1541] [Topology ] . ( 332 sec) [ -20102.1543] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 388 sec) [ -20898.1075] [Alpha ][ 1.719622] . ( 389 sec) [ -20895.9923] [ 4555] [depth= 1] . ( 390 sec) [ -20889.3372] [ 4547] [depth= 2] . ( 391 sec) [ -20888.5728] [ 4552] [depth= 1] . ( 392 sec) [ -20867.7868] [ 4559] [depth= 3] . ( 393 sec) [ -20856.0045] [ 4569] [depth= 1] . ( 394 sec) [ -20765.8045] [ 4559] [depth= 1] . ( 394 sec) [ -20510.5376] [ 4542] [depth= 1] . ( 395 sec) [ -20497.8122] [ 4539] [depth= 1] . ( 395 sec) [ -20290.4169] [ 4535] [depth= 1] . ( 396 sec) [ -20246.4177] [ 4531] [depth= 1] . ( 397 sec) [ -20210.5193] [ 4535] [depth= 2] . ( 399 sec) [ -20210.2034] [ 4539] [depth= 1] . ( 400 sec) [ -20130.0567] [Branch lengths ] . ( 401 sec) [ -20128.9883] [Alpha ][ 1.563589] . ( 404 sec) [ -20127.4467] [ 4540] [depth= 1] . ( 405 sec) [ -20125.9501] [ 4537] [depth= 1] . ( 410 sec) [ -20121.8097] [ 4532] [depth= 1] . ( 412 sec) [ -20120.1590] [ 4532] [depth= 1] . ( 414 sec) [ -20119.7832] [ 4532] [depth= 1] . ( 418 sec) [ -20105.7485] [Branch lengths ] . ( 419 sec) [ -20104.0472] [Alpha ][ 1.399967] . ( 431 sec) [ -20104.0291] [ 4532] [depth= 1] . ( 435 sec) [ -20100.3666] [Branch lengths ] . ( 435 sec) [ -20099.9527] [Alpha ][ 1.328237] . ( 450 sec) [ -20099.8226] [ 4532] [depth= 1] . ( 454 sec) [ -20099.0255] [Branch lengths ] . ( 455 sec) [ -20098.9412] [Alpha ][ 1.298255] . ( 471 sec) [ -20098.5912] [Branch lengths ] . ( 471 sec) [ -20098.5912] [Topology ] . ( 473 sec) [ -20098.5244] [Topology ] . ( 475 sec) [ -20098.4864] [Topology ] . ( 477 sec) [ -20098.4592] [Topology ] . ( 479 sec) [ -20098.4386] [Topology ] . ( 481 sec) [ -20098.4225] [Topology ] . ( 483 sec) [ -20098.4097] [Topology ] . ( 484 sec) [ -20098.3651] [Alpha ][ 1.276249] . ( 484 sec) [ -20098.3651] [Topology ] . ( 486 sec) [ -20098.3366] [Topology ] . ( 488 sec) [ -20098.3233] [Topology ] . ( 490 sec) [ -20098.3143] [Topology ] . ( 492 sec) [ -20098.3074] [Topology ] . ( 494 sec) [ -20098.3019] [Topology ] . ( 496 sec) [ -20098.2973] [Topology ] . ( 496 sec) [ -20098.2870] [Alpha ][ 1.265798] . ( 496 sec) [ -20098.2870] [Topology ] . ( 498 sec) [ -20098.2784] [Topology ] . ( 500 sec) [ -20098.2738] [Topology ] . ( 502 sec) [ -20098.2704] [Topology ] . ( 504 sec) [ -20098.2676] [Topology ] . ( 506 sec) [ -20098.2654] [Topology ] . ( 508 sec) [ -20098.2634] [Topology ] . ( 508 sec) [ -20098.2606] [Alpha ][ 1.260348] . ( 508 sec) [ -20098.2606] [Topology ] . ( 510 sec) [ -20098.2575] [Topology ] . ( 512 sec) [ -20098.2557] [Topology ] . ( 514 sec) [ -20098.2542] [Topology ] . ( 516 sec) [ -20098.2530] [Topology ] . ( 518 sec) [ -20098.2519] [Topology ] . ( 520 sec) [ -20098.2510] [Topology ] . ( 521 sec) [ -20098.2502] [Alpha ][ 1.257423] . ( 521 sec) [ -20098.2502] [Topology ] . ( 523 sec) [ -20098.2490] [Topology ] . ( 525 sec) [ -20098.2482] [Topology ] . ( 525 sec) [ -20098.2481] [Alpha ][ 1.256165] . ( 525 sec) [ -20098.2481] [Topology ] . ( 527 sec) [ -20098.2473] [Topology ] . ( 528 sec) [ -20098.2473] [Alpha ][ 1.254909] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -20102.154256 . Log likelihood obtained after SPR moves : -20098.247253 . Log likelihood of the current tree: -20098.247253. . Printing the most likely tree in file 'proteic_M2512_14x717_2006.phy_phyml_tree.txt'... . Best log likelihood : -20098.246766 . Time used 0h9m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1512.31user 0.00system 25:18.32elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps