.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1499_22x513_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... . 440 patterns found. (out of a total of 513 sites) . 87 sites without polymorphism (16.96%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15800.7213] [Alpha ][ 0.500960] . ( 1 sec) [ -15467.2074] [ 2873] [depth= 12] . ( 2 sec) [ -15264.8749] [ 2834] [depth= 10] . ( 2 sec) [ -15178.7833] [ 2797] [depth= 9] . ( 3 sec) [ -15055.1189] [ 2761] [depth= 1] . ( 3 sec) [ -14835.1353] [ 2755] [depth= 6] . ( 3 sec) [ -14743.4479] [ 2753] [depth= 1] . ( 3 sec) [ -14541.3849] [ 2755] [depth= 3] . ( 4 sec) [ -14480.3223] [ 2734] [depth= 1] . ( 4 sec) [ -14425.1555] [ 2700] [depth= 2] . ( 4 sec) [ -14414.7997] [ 2699] [depth= 1] . ( 5 sec) [ -14394.2877] [ 2686] [depth= 3] . ( 5 sec) [ -14368.7354] [ 2677] [depth= 1] . ( 5 sec) [ -14275.2573] [ 2652] [depth= 6] . ( 5 sec) [ -14230.1508] [ 2658] [depth= 1] . ( 6 sec) [ -14074.3007] [ 2645] [depth= 5] . ( 6 sec) [ -13944.5127] [ 2637] [depth= 1] . ( 6 sec) [ -13872.4375] [ 2625] [depth= 1] . ( 7 sec) [ -13872.0995] [ 2626] [depth= 2] . ( 7 sec) [ -13815.9965] [ 2633] [depth= 1] . ( 7 sec) [ -13788.8049] [ 2617] [depth= 4] . ( 8 sec) [ -13632.3741] [ 2571] [depth= 5] . ( 8 sec) [ -13625.5781] [ 2580] [depth= 1] . ( 8 sec) [ -13504.4319] [ 2564] [depth= 2] . ( 9 sec) [ -13485.3134] [ 2563] [depth= 1] . ( 9 sec) [ -13479.7758] [ 2565] [depth= 1] . ( 9 sec) [ -13383.1553] [ 2559] [depth= 2] . ( 10 sec) [ -13374.3325] [ 2564] [depth= 1] . ( 10 sec) [ -13329.4886] [ 2544] [depth= 2] . ( 10 sec) [ -13267.4526] [ 2512] [depth= 6] . ( 11 sec) [ -13098.1449] [ 2472] [depth= 1] . ( 11 sec) [ -12950.4143] [ 2431] [depth= 9] . ( 11 sec) [ -12935.6826] [ 2432] [depth= 1] . ( 12 sec) [ -12902.5704] [ 2426] [depth= 1] . ( 12 sec) [ -12901.0736] [ 2422] [depth= 1] . ( 12 sec) [ -12872.4874] [ 2397] [depth= 3] . ( 13 sec) [ -12731.9413] [ 2354] [depth= 1] . ( 13 sec) [ -12725.7976] [ 2354] [depth= 1] . ( 14 sec) [ -12653.4571] [ 2356] [depth= 1] . ( 15 sec) [ -12647.7617] [ 2354] [depth= 1] . ( 15 sec) [ -12647.7134] [ 2358] [depth= 1] . ( 16 sec) [ -12635.3502] [ 2359] [depth= 1] . ( 16 sec) [ -12584.2282] [ 2345] [depth= 1] . ( 17 sec) [ -12583.6010] [ 2348] [depth= 1] . ( 18 sec) [ -12578.5998] [ 2354] [depth= 1] . ( 19 sec) [ -12552.0061] [Branch lengths ] . ( 19 sec) [ -12507.4714] [Alpha ][ 0.951605] . ( 20 sec) [ -12506.4512] [ 2347] [depth= 2] . ( 20 sec) [ -12505.8808] [ 2348] [depth= 1] . ( 23 sec) [ -12499.6429] [ 2346] [depth= 1] . ( 23 sec) [ -12497.4093] [ 2343] [depth= 2] . ( 24 sec) [ -12495.8026] [ 2343] [depth= 1] . ( 27 sec) [ -12487.3350] [ 2338] [depth= 1] . ( 30 sec) [ -12485.6278] [ 2338] [depth= 1] . ( 41 sec) [ -12475.3727] [Branch lengths ] . ( 41 sec) [ -12475.2375] [Alpha ][ 0.988159] . ( 63 sec) [ -12473.7058] [Branch lengths ] . ( 63 sec) [ -12473.7058] [Topology ] . ( 65 sec) [ -12472.4288] [Topology ] . ( 66 sec) [ -12471.7695] [Topology ] . ( 68 sec) [ -12471.6957] [Topology ] . ( 70 sec) [ -12471.6732] [Topology ] . ( 72 sec) [ -12471.6636] [Topology ] . ( 74 sec) [ -12471.6587] [Topology ] . ( 76 sec) [ -12471.6561] [Topology ] . ( 76 sec) [ -12471.6421] [Alpha ][ 1.000197] . ( 76 sec) [ -12471.6421] [Topology ] . ( 78 sec) [ -12471.6404] [Topology ] . ( 80 sec) [ -12471.6395] [Topology ] . ( 80 sec) [ -12471.6395] [Alpha ][ 1.000197] . ( 80 sec) [ -12471.6395] [Topology ] . ( 82 sec) [ -12471.6389] [Topology ] . ( 82 sec) [ -12471.6389] [Alpha ][ 1.000197] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12471.638941. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15881.2557] [Alpha ][ 0.500960] . ( 1 sec) [ -15685.6962] [ 2869] [depth= 2] . ( 1 sec) [ -15457.0682] [ 2851] [depth= 6] . ( 1 sec) [ -15385.8797] [ 2851] [depth= 1] . ( 2 sec) [ -15310.3702] [ 2843] [depth= 3] . ( 2 sec) [ -15238.5939] [ 2820] [depth= 2] . ( 2 sec) [ -15147.5115] [ 2809] [depth= 6] . ( 3 sec) [ -15037.6488] [ 2773] [depth= 2] . ( 3 sec) [ -14940.0908] [ 2771] [depth= 2] . ( 3 sec) [ -14882.6049] [ 2765] [depth= 1] . ( 4 sec) [ -14862.2212] [ 2759] [depth= 2] . ( 4 sec) [ -14841.3731] [ 2755] [depth= 1] . ( 4 sec) [ -14703.6585] [ 2712] [depth= 7] . ( 5 sec) [ -14703.2927] [ 2713] [depth= 1] . ( 5 sec) [ -14308.0122] [ 2620] [depth= 6] . ( 5 sec) [ -14004.2485] [ 2614] [depth= 2] . ( 6 sec) [ -13983.8334] [ 2615] [depth= 1] . ( 6 sec) [ -13955.9064] [ 2596] [depth= 1] . ( 6 sec) [ -13839.9224] [ 2580] [depth= 4] . ( 7 sec) [ -13824.5613] [ 2578] [depth= 1] . ( 7 sec) [ -13657.3096] [ 2528] [depth= 6] . ( 7 sec) [ -13577.6625] [ 2531] [depth= 3] . ( 8 sec) [ -13549.4606] [ 2528] [depth= 1] . ( 8 sec) [ -13418.0194] [ 2494] [depth= 2] . ( 9 sec) [ -13231.3508] [ 2437] [depth= 4] . ( 9 sec) [ -13228.3343] [ 2438] [depth= 1] . ( 9 sec) [ -13199.2116] [ 2428] [depth= 1] . ( 10 sec) [ -13166.0019] [ 2420] [depth= 2] . ( 10 sec) [ -13115.1643] [ 2399] [depth= 1] . ( 10 sec) [ -13086.4296] [ 2390] [depth= 2] . ( 11 sec) [ -12823.3417] [ 2384] [depth= 3] . ( 12 sec) [ -12817.4304] [ 2383] [depth= 3] . ( 12 sec) [ -12763.2808] [ 2365] [depth= 2] . ( 12 sec) [ -12760.4273] [ 2365] [depth= 1] . ( 12 sec) [ -12746.4792] [ 2370] [depth= 5] . ( 13 sec) [ -12741.3311] [ 2371] [depth= 1] . ( 13 sec) [ -12735.8202] [ 2370] [depth= 1] . ( 14 sec) [ -12732.0053] [ 2371] [depth= 2] . ( 14 sec) [ -12715.9246] [ 2371] [depth= 1] . ( 15 sec) [ -12713.1879] [ 2371] [depth= 1] . ( 15 sec) [ -12702.0256] [ 2371] [depth= 1] . ( 16 sec) [ -12698.4583] [ 2371] [depth= 1] . ( 16 sec) [ -12647.4455] [ 2353] [depth= 1] . ( 17 sec) [ -12583.5453] [Branch lengths ] . ( 17 sec) [ -12542.4106] [Alpha ][ 0.930044] . ( 21 sec) [ -12526.7491] [ 2344] [depth= 1] . ( 23 sec) [ -12526.1084] [ 2348] [depth= 1] . ( 26 sec) [ -12512.5620] [ 2344] [depth= 1] . ( 26 sec) [ -12511.5643] [ 2344] [depth= 1] . ( 26 sec) [ -12492.3468] [ 2339] [depth= 1] . ( 28 sec) [ -12489.8781] [ 2338] [depth= 2] . ( 31 sec) [ -12489.8193] [ 2339] [depth= 1] . ( 32 sec) [ -12489.4693] [ 2339] [depth= 1] . ( 37 sec) [ -12478.6245] [Branch lengths ] . ( 38 sec) [ -12478.2714] [Alpha ][ 0.987656] . ( 46 sec) [ -12477.2646] [ 2339] [depth= 1] . ( 53 sec) [ -12477.2114] [ 2338] [depth= 1] . ( 58 sec) [ -12474.0986] [Branch lengths ] . ( 59 sec) [ -12474.0944] [Alpha ][ 0.994248] . ( 80 sec) [ -12473.4381] [Branch lengths ] . ( 80 sec) [ -12473.4381] [Topology ] . ( 82 sec) [ -12472.2960] [Topology ] . ( 84 sec) [ -12471.7081] [Topology ] . ( 86 sec) [ -12471.6588] [Topology ] . ( 87 sec) [ -12471.6480] [Topology ] . ( 89 sec) [ -12471.6446] [Topology ] . ( 91 sec) [ -12471.6432] [Topology ] . ( 93 sec) [ -12471.6425] [Topology ] . ( 93 sec) [ -12471.6392] [Alpha ][ 1.000125] . ( 93 sec) [ -12471.6392] [Topology ] . ( 95 sec) [ -12471.6388] [Topology ] . ( 96 sec) [ -12471.6388] [Alpha ][ 1.000125] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12471.638753. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15931.7531] [Alpha ][ 0.500960] . ( 1 sec) [ -15738.8347] [ 2923] [depth= 6] . ( 1 sec) [ -15315.6340] [ 2876] [depth= 5] . ( 2 sec) [ -15230.6893] [ 2857] [depth= 2] . ( 2 sec) [ -15150.4619] [ 2828] [depth= 1] . ( 2 sec) [ -14910.1311] [ 2821] [depth= 1] . ( 3 sec) [ -14819.7208] [ 2817] [depth= 1] . ( 3 sec) [ -14743.2967] [ 2797] [depth= 3] . ( 4 sec) [ -14741.7723] [ 2780] [depth= 4] . ( 4 sec) [ -14593.6957] [ 2762] [depth= 1] . ( 4 sec) [ -14591.4419] [ 2760] [depth= 1] . ( 5 sec) [ -14455.0676] [ 2720] [depth= 5] . ( 5 sec) [ -14391.8433] [ 2734] [depth= 1] . ( 5 sec) [ -14374.1917] [ 2735] [depth= 8] . ( 6 sec) [ -14166.0017] [ 2644] [depth= 10] . ( 6 sec) [ -14160.7106] [ 2646] [depth= 1] . ( 6 sec) [ -14127.8227] [ 2632] [depth= 1] . ( 7 sec) [ -13994.5844] [ 2593] [depth= 6] . ( 7 sec) [ -13936.9906] [ 2589] [depth= 5] . ( 7 sec) [ -13851.5639] [ 2591] [depth= 1] . ( 8 sec) [ -13763.8763] [ 2581] [depth= 2] . ( 8 sec) [ -13759.5104] [ 2585] [depth= 1] . ( 9 sec) [ -13759.3536] [ 2587] [depth= 6] . ( 9 sec) [ -13757.8024] [ 2590] [depth= 4] . ( 9 sec) [ -13656.4507] [ 2566] [depth= 2] . ( 10 sec) [ -13612.7537] [ 2566] [depth= 1] . ( 10 sec) [ -13591.0942] [ 2568] [depth= 3] . ( 11 sec) [ -13586.0545] [ 2564] [depth= 2] . ( 11 sec) [ -13453.4689] [ 2573] [depth= 1] . ( 11 sec) [ -13433.9070] [ 2564] [depth= 1] . ( 12 sec) [ -13228.6757] [ 2492] [depth= 4] . ( 12 sec) [ -13084.6412] [ 2454] [depth= 9] . ( 12 sec) [ -13082.4779] [ 2456] [depth= 1] . ( 13 sec) [ -13069.9340] [ 2457] [depth= 6] . ( 13 sec) [ -12938.0950] [ 2413] [depth= 3] . ( 13 sec) [ -12820.3548] [ 2365] [depth= 2] . ( 14 sec) [ -12804.9350] [ 2359] [depth= 2] . ( 14 sec) [ -12792.1168] [ 2351] [depth= 2] . ( 14 sec) [ -12771.8165] [ 2347] [depth= 2] . ( 15 sec) [ -12766.8366] [ 2343] [depth= 1] . ( 16 sec) [ -12738.7843] [ 2343] [depth= 3] . ( 16 sec) [ -12720.5323] [ 2339] [depth= 2] . ( 17 sec) [ -12719.3475] [ 2339] [depth= 1] . ( 18 sec) [ -12557.2834] [Branch lengths ] . ( 18 sec) [ -12512.6957] [Alpha ][ 0.952980] . ( 20 sec) [ -12499.1098] [ 2339] [depth= 1] . ( 21 sec) [ -12497.8833] [ 2338] [depth= 1] . ( 23 sec) [ -12497.1121] [ 2341] [depth= 1] . ( 24 sec) [ -12497.0280] [ 2341] [depth= 1] . ( 30 sec) [ -12496.7793] [ 2341] [depth= 1] . ( 35 sec) [ -12496.1817] [ 2341] [depth= 1] . ( 36 sec) [ -12496.1500] [ 2341] [depth= 1] . ( 41 sec) [ -12477.3083] [Branch lengths ] . ( 41 sec) [ -12477.2026] [Alpha ][ 0.984763] . ( 50 sec) [ -12477.1428] [ 2338] [depth= 2] . ( 63 sec) [ -12474.0200] [Branch lengths ] . ( 63 sec) [ -12474.0089] [Alpha ][ 0.995528] . ( 84 sec) [ -12473.4115] [Branch lengths ] . ( 84 sec) [ -12473.4115] [Topology ] . ( 86 sec) [ -12472.3066] [Topology ] . ( 88 sec) [ -12471.7070] [Topology ] . ( 90 sec) [ -12471.6560] [Topology ] . ( 92 sec) [ -12471.6456] [Topology ] . ( 94 sec) [ -12471.6426] [Topology ] . ( 95 sec) [ -12471.6415] [Topology ] . ( 97 sec) [ -12471.6410] [Topology ] . ( 98 sec) [ -12471.6389] [Alpha ][ 1.000104] . ( 98 sec) [ -12471.6389] [Topology ] . ( 100 sec) [ -12471.6386] [Topology ] . ( 100 sec) [ -12471.6386] [Alpha ][ 1.000104] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12471.638612. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15663.8199] [Alpha ][ 0.506300] . ( 1 sec) [ -15523.5012] [ 2932] [depth= 5] . ( 1 sec) [ -15230.8651] [ 2866] [depth= 5] . ( 1 sec) [ -15036.4675] [ 2861] [depth= 1] . ( 2 sec) [ -15002.8223] [ 2863] [depth= 1] . ( 2 sec) [ -14889.3985] [ 2846] [depth= 5] . ( 2 sec) [ -14792.5378] [ 2827] [depth= 2] . ( 3 sec) [ -14767.0786] [ 2829] [depth= 4] . ( 3 sec) [ -14715.4825] [ 2829] [depth= 1] . ( 3 sec) [ -14703.5324] [ 2794] [depth= 5] . ( 3 sec) [ -14494.0930] [ 2737] [depth= 4] . ( 4 sec) [ -14448.6608] [ 2722] [depth= 11] . ( 4 sec) [ -14202.3328] [ 2659] [depth= 3] . ( 5 sec) [ -14062.1738] [ 2656] [depth= 1] . ( 5 sec) [ -13894.8551] [ 2607] [depth= 5] . ( 6 sec) [ -13727.8788] [ 2553] [depth= 3] . ( 6 sec) [ -13699.5409] [ 2540] [depth= 6] . ( 6 sec) [ -13696.5538] [ 2540] [depth= 1] . ( 6 sec) [ -13693.8490] [ 2547] [depth= 1] . ( 7 sec) [ -13614.7685] [ 2533] [depth= 9] . ( 7 sec) [ -13585.4620] [ 2517] [depth= 1] . ( 7 sec) [ -13527.4591] [ 2491] [depth= 4] . ( 8 sec) [ -13509.3469] [ 2482] [depth= 2] . ( 8 sec) [ -13222.7948] [ 2446] [depth= 1] . ( 9 sec) [ -13125.6194] [ 2426] [depth= 1] . ( 9 sec) [ -13065.2885] [ 2387] [depth= 2] . ( 10 sec) [ -12813.3987] [ 2367] [depth= 3] . ( 10 sec) [ -12806.4427] [ 2371] [depth= 1] . ( 10 sec) [ -12806.2248] [ 2366] [depth= 2] . ( 11 sec) [ -12806.1381] [ 2368] [depth= 1] . ( 11 sec) [ -12797.8284] [ 2371] [depth= 1] . ( 11 sec) [ -12678.2212] [ 2347] [depth= 2] . ( 12 sec) [ -12667.3605] [ 2346] [depth= 1] . ( 12 sec) [ -12647.6872] [ 2339] [depth= 1] . ( 13 sec) [ -12644.6154] [ 2338] [depth= 1] . ( 14 sec) [ -12643.4122] [ 2337] [depth= 1] . ( 14 sec) [ -12616.0875] [ 2334] [depth= 1] . ( 15 sec) [ -12610.7207] [ 2334] [depth= 1] . ( 17 sec) [ -12603.3834] [ 2338] [depth= 1] . ( 18 sec) [ -12542.1908] [Branch lengths ] . ( 18 sec) [ -12501.8078] [Alpha ][ 0.932533] . ( 21 sec) [ -12498.3475] [ 2336] [depth= 1] . ( 24 sec) [ -12496.2775] [ 2334] [depth= 2] . ( 26 sec) [ -12494.6763] [ 2338] [depth= 2] . ( 28 sec) [ -12494.5199] [ 2338] [depth= 1] . ( 35 sec) [ -12494.4001] [ 2338] [depth= 1] . ( 35 sec) [ -12493.2043] [ 2337] [depth= 1] . ( 39 sec) [ -12474.0526] [Branch lengths ] . ( 39 sec) [ -12473.6835] [Alpha ][ 0.991446] . ( 61 sec) [ -12471.9920] [Branch lengths ] . ( 61 sec) [ -12471.9920] [Topology ] . ( 63 sec) [ -12471.7942] [Topology ] . ( 65 sec) [ -12471.7266] [Topology ] . ( 67 sec) [ -12471.6912] [Topology ] . ( 69 sec) [ -12471.6715] [Topology ] . ( 71 sec) [ -12471.6604] [Topology ] . ( 72 sec) [ -12471.6541] [Topology ] . ( 73 sec) [ -12471.6470] [Alpha ][ 1.000051] . ( 73 sec) [ -12471.6470] [Topology ] . ( 75 sec) [ -12471.6432] [Topology ] . ( 77 sec) [ -12471.6411] [Topology ] . ( 78 sec) [ -12471.6399] [Topology ] . ( 80 sec) [ -12471.6392] [Topology ] . ( 81 sec) [ -12471.6392] [Alpha ][ 1.000051] . ( 81 sec) [ -12471.6392] [Topology ] . ( 83 sec) [ -12471.6388] [Topology ] . ( 83 sec) [ -12471.6388] [Alpha ][ 1.000051] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12471.638771. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15379.3880] [Alpha ][ 0.500960] . ( 1 sec) [ -15048.6472] [ 2779] [depth= 9] . ( 2 sec) [ -15008.5689] [ 2792] [depth= 5] . ( 2 sec) [ -14901.9964] [ 2787] [depth= 7] . ( 2 sec) [ -14868.7813] [ 2786] [depth= 1] . ( 3 sec) [ -14745.2762] [ 2736] [depth= 7] . ( 3 sec) [ -14276.6266] [ 2680] [depth= 4] . ( 3 sec) [ -14144.6529] [ 2658] [depth= 1] . ( 4 sec) [ -13960.1853] [ 2610] [depth= 8] . ( 4 sec) [ -13917.2755] [ 2598] [depth= 2] . ( 4 sec) [ -13822.5806] [ 2593] [depth= 1] . ( 5 sec) [ -13791.5524] [ 2589] [depth= 1] . ( 5 sec) [ -13629.1343] [ 2582] [depth= 2] . ( 5 sec) [ -13621.2904] [ 2578] [depth= 2] . ( 5 sec) [ -13572.1646] [ 2563] [depth= 2] . ( 6 sec) [ -13519.2085] [ 2547] [depth= 1] . ( 6 sec) [ -13418.8149] [ 2512] [depth= 3] . ( 6 sec) [ -13415.9768] [ 2512] [depth= 1] . ( 7 sec) [ -13411.9665] [ 2511] [depth= 1] . ( 7 sec) [ -13384.2804] [ 2499] [depth= 1] . ( 7 sec) [ -13344.7710] [ 2483] [depth= 1] . ( 8 sec) [ -13275.3764] [ 2479] [depth= 2] . ( 8 sec) [ -13068.7015] [ 2455] [depth= 3] . ( 8 sec) [ -12903.7895] [ 2415] [depth= 1] . ( 9 sec) [ -12901.7257] [ 2419] [depth= 1] . ( 9 sec) [ -12873.3063] [ 2412] [depth= 2] . ( 10 sec) [ -12840.5601] [ 2393] [depth= 2] . ( 11 sec) [ -12805.8319] [ 2380] [depth= 2] . ( 11 sec) [ -12805.0605] [ 2380] [depth= 1] . ( 11 sec) [ -12795.9280] [ 2374] [depth= 3] . ( 12 sec) [ -12730.1742] [ 2356] [depth= 2] . ( 12 sec) [ -12724.9912] [ 2346] [depth= 4] . ( 13 sec) [ -12688.3707] [ 2335] [depth= 2] . ( 15 sec) [ -12686.1534] [ 2333] [depth= 1] . ( 16 sec) [ -12685.2417] [ 2334] [depth= 1] . ( 16 sec) [ -12676.0588] [ 2334] [depth= 1] . ( 17 sec) [ -12674.2192] [ 2339] [depth= 1] . ( 17 sec) [ -12672.6559] [ 2334] [depth= 1] . ( 19 sec) [ -12670.3872] [ 2338] [depth= 1] . ( 20 sec) [ -12560.0595] [Branch lengths ] . ( 20 sec) [ -12517.2551] [Alpha ][ 0.938970] . ( 27 sec) [ -12515.2777] [ 2334] [depth= 1] . ( 28 sec) [ -12513.8233] [ 2339] [depth= 3] . ( 30 sec) [ -12510.0333] [ 2342] [depth= 1] . ( 30 sec) [ -12502.3440] [ 2340] [depth= 1] . ( 32 sec) [ -12501.9304] [ 2338] [depth= 1] . ( 32 sec) [ -12500.1612] [ 2337] [depth= 1] . ( 35 sec) [ -12499.8498] [ 2337] [depth= 1] . ( 40 sec) [ -12473.9044] [Branch lengths ] . ( 40 sec) [ -12473.5901] [Alpha ][ 0.993542] . ( 62 sec) [ -12471.8735] [Branch lengths ] . ( 62 sec) [ -12471.8735] [Topology ] . ( 64 sec) [ -12471.7511] [Topology ] . ( 66 sec) [ -12471.7027] [Topology ] . ( 68 sec) [ -12471.6764] [Topology ] . ( 69 sec) [ -12471.6618] [Topology ] . ( 71 sec) [ -12471.6535] [Topology ] . ( 73 sec) [ -12471.6488] [Topology ] . ( 74 sec) [ -12471.6448] [Alpha ][ 1.000036] . ( 74 sec) [ -12471.6448] [Topology ] . ( 76 sec) [ -12471.6419] [Topology ] . ( 77 sec) [ -12471.6404] [Topology ] . ( 79 sec) [ -12471.6394] [Topology ] . ( 79 sec) [ -12471.6394] [Alpha ][ 1.000036] . ( 80 sec) [ -12471.6394] [Topology ] . ( 81 sec) [ -12471.6389] [Topology ] . ( 82 sec) [ -12471.6389] [Alpha ][ 1.000036] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12471.638931. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -12557.6395] [Alpha ][ 0.856477] . ( 1 sec) [ -12557.6395] [Topology ] . ( 2 sec) [ -12484.9190] [Topology ] . ( 4 sec) [ -12478.1976] [Topology ] . ( 6 sec) [ -12476.2470] [Topology ] . ( 8 sec) [ -12475.3143] [Topology ] . ( 10 sec) [ -12474.7983] [Topology ] . ( 12 sec) [ -12474.4984] [Topology ] . Checking for NNIs, optimizing five branches... . ( 28 sec) [ -12472.2624] [Alpha ][ 0.994811] . ( 28 sec) [ -12472.2624] [Topology ] . ( 30 sec) [ -12471.9802] [Topology ] . ( 32 sec) [ -12471.8311] [Topology ] . ( 33 sec) [ -12471.7482] [Topology ] . ( 35 sec) [ -12471.7019] [Topology ] . ( 37 sec) [ -12471.6755] [Topology ] . ( 39 sec) [ -12471.6607] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -12471.6582] [Alpha ][ 0.999840] . ( 55 sec) [ -12471.6582] [Topology ] . ( 57 sec) [ -12471.6496] [Topology ] . ( 59 sec) [ -12471.6447] [Topology ] . ( 61 sec) [ -12471.6419] [Topology ] . ( 62 sec) [ -12471.6404] [Topology ] . ( 64 sec) [ -12471.6395] [Topology ] . Checking for NNIs, optimizing five branches... . ( 80 sec) [ -12471.6395] [Alpha ][ 0.999840] . ( 80 sec) [ -12471.6395] [Topology ] . ( 82 sec) [ -12471.6389] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 114 sec) [ -12557.6395] [Alpha ][ 0.856477] . ( 118 sec) [ -12555.7312] [ 2338] [depth= 1] . ( 119 sec) [ -12555.3621] [ 2338] [depth= 1] . ( 120 sec) [ -12552.4390] [ 2338] [depth= 1] . ( 120 sec) [ -12543.7453] [ 2338] [depth= 1] . ( 121 sec) [ -12536.4678] [ 2338] [depth= 1] . ( 122 sec) [ -12533.0242] [ 2339] [depth= 1] . ( 122 sec) [ -12530.6027] [ 2340] [depth= 1] . ( 123 sec) [ -12525.0215] [ 2339] [depth= 1] . ( 125 sec) [ -12524.3564] [ 2343] [depth= 1] . ( 125 sec) [ -12513.4581] [ 2339] [depth= 1] . ( 128 sec) [ -12509.8724] [ 2341] [depth= 1] . ( 131 sec) [ -12507.5321] [ 2339] [depth= 1] . ( 133 sec) [ -12481.1962] [Branch lengths ] . ( 133 sec) [ -12479.6864] [Alpha ][ 0.969158] . ( 155 sec) [ -12475.3112] [Branch lengths ] . ( 156 sec) [ -12475.3112] [Topology ] . ( 157 sec) [ -12473.0541] [Topology ] . ( 159 sec) [ -12472.0492] [Topology ] . ( 161 sec) [ -12471.8833] [Topology ] . ( 163 sec) [ -12471.8153] [Topology ] . ( 165 sec) [ -12471.7806] [Topology ] . ( 167 sec) [ -12471.7614] [Topology ] . ( 168 sec) [ -12471.7506] [Topology ] . ( 169 sec) [ -12471.6554] [Alpha ][ 0.999427] . ( 169 sec) [ -12471.6554] [Topology ] . ( 171 sec) [ -12471.6478] [Topology ] . ( 173 sec) [ -12471.6437] [Topology ] . ( 174 sec) [ -12471.6414] [Topology ] . ( 176 sec) [ -12471.6401] [Topology ] . ( 178 sec) [ -12471.6393] [Topology ] . ( 178 sec) [ -12471.6393] [Alpha ][ 1.000426] . ( 178 sec) [ -12471.6393] [Topology ] . ( 180 sec) [ -12471.6388] [Topology ] . ( 181 sec) [ -12471.6388] [Alpha ][ 1.000426] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12471.638936 . Log likelihood obtained after SPR moves : -12471.638827 . Log likelihood of the current tree: -12471.638827. . Printing the most likely tree in file 'proteic_M1499_22x513_2003.phy_phyml_tree.txt'... . Best log likelihood : -12471.638612 . Time used 0h3m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 710.56user 0.00system 12:01.67elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps