.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2733_60x1207_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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... . 564 patterns found. (out of a total of 1207 sites) . 771 sites without polymorphism (63.88%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22498.7352] [GTR parameters ] . ( 1 sec) [ -21918.9830] [Alpha ][ 0.500960] . ( 1 sec) [ -21686.6410] [ 3368] [depth= 8] . ( 2 sec) [ -21485.8667] [ 3301] [depth= 4] . ( 2 sec) [ -21427.6337] [ 3292] [depth= 3] . ( 2 sec) [ -21268.1273] [ 3272] [depth= 1] . ( 2 sec) [ -21196.3005] [ 3265] [depth= 5] . ( 2 sec) [ -21142.0659] [ 3261] [depth= 2] . ( 2 sec) [ -21142.0180] [ 3259] [depth= 3] . ( 2 sec) [ -21046.4352] [ 3259] [depth= 7] . ( 2 sec) [ -21036.0441] [ 3255] [depth= 2] . ( 2 sec) [ -21023.5958] [ 3246] [depth= 8] . ( 2 sec) [ -20973.7016] [ 3234] [depth= 2] . ( 2 sec) [ -20907.7409] [ 3212] [depth= 11] . ( 2 sec) [ -20630.9690] [ 3185] [depth= 7] . ( 2 sec) [ -20433.4570] [ 3183] [depth= 1] . ( 3 sec) [ -19954.4649] [ 3150] [depth= 4] . ( 3 sec) [ -19607.7973] [ 3115] [depth= 7] . ( 3 sec) [ -19476.7975] [ 3068] [depth= 1] . ( 3 sec) [ -19340.2520] [ 3049] [depth= 9] . ( 3 sec) [ -19208.0711] [ 3036] [depth= 1] . ( 3 sec) [ -18422.5154] [ 2988] [depth= 10] . ( 3 sec) [ -18164.7947] [ 2980] [depth= 1] . ( 3 sec) [ -18076.5639] [ 2956] [depth= 1] . ( 3 sec) [ -18000.1581] [ 2951] [depth= 8] . ( 3 sec) [ -17941.2565] [ 2955] [depth= 14] . ( 4 sec) [ -17833.0919] [ 2916] [depth= 14] . ( 4 sec) [ -17650.8842] [ 2887] [depth= 11] . ( 4 sec) [ -17637.7074] [ 2885] [depth= 2] . ( 4 sec) [ -17594.8579] [ 2872] [depth= 6] . ( 4 sec) [ -17588.5552] [ 2873] [depth= 1] . ( 4 sec) [ -17440.2892] [ 2868] [depth= 11] . ( 4 sec) [ -17093.9066] [ 2799] [depth= 6] . ( 4 sec) [ -16960.5956] [ 2766] [depth= 6] . ( 4 sec) [ -16945.6894] [ 2761] [depth= 1] . ( 4 sec) [ -16929.5613] [ 2757] [depth= 5] . ( 4 sec) [ -16914.0259] [ 2756] [depth= 1] . ( 5 sec) [ -16789.6129] [ 2738] [depth= 13] . ( 5 sec) [ -16593.4846] [ 2720] [depth= 1] . ( 5 sec) [ -16428.6356] [ 2687] [depth= 1] . ( 5 sec) [ -16068.4295] [ 2665] [depth= 9] . ( 5 sec) [ -15936.2623] [ 2647] [depth= 7] . ( 5 sec) [ -15733.4575] [ 2640] [depth= 1] . ( 5 sec) [ -15327.9278] [ 2623] [depth= 11] . ( 5 sec) [ -15235.4781] [ 2601] [depth= 1] . ( 5 sec) [ -15205.2103] [ 2590] [depth= 9] . ( 5 sec) [ -15204.2794] [ 2590] [depth= 1] . ( 5 sec) [ -15189.0851] [ 2590] [depth= 14] . ( 5 sec) [ -15116.2003] [ 2564] [depth= 1] . ( 5 sec) [ -15000.2775] [ 2560] [depth= 9] . ( 6 sec) [ -14693.7706] [ 2492] [depth= 12] . ( 6 sec) [ -14692.6803] [ 2492] [depth= 1] . ( 6 sec) [ -14664.1503] [ 2485] [depth= 9] . ( 6 sec) [ -14639.0329] [ 2481] [depth= 1] . ( 6 sec) [ -14589.4230] [ 2477] [depth= 2] . ( 6 sec) [ -14566.4137] [ 2469] [depth= 1] . ( 6 sec) [ -14561.5292] [ 2465] [depth= 2] . ( 6 sec) [ -14539.9967] [ 2463] [depth= 2] . ( 6 sec) [ -14468.4692] [ 2460] [depth= 3] . ( 7 sec) [ -14459.1560] [ 2456] [depth= 4] . ( 7 sec) [ -14423.5168] [ 2454] [depth= 4] . ( 7 sec) [ -14238.3333] [ 2390] [depth= 1] . ( 7 sec) [ -14211.8349] [ 2387] [depth= 4] . ( 7 sec) [ -14174.4747] [ 2372] [depth= 1] . ( 7 sec) [ -14140.5978] [ 2343] [depth= 15] . ( 7 sec) [ -14132.1841] [ 2336] [depth= 6] . ( 7 sec) [ -14089.6569] [ 2327] [depth= 7] . ( 7 sec) [ -14064.5339] [ 2326] [depth= 7] . ( 7 sec) [ -14041.7161] [ 2325] [depth= 1] . ( 8 sec) [ -13956.6183] [ 2302] [depth= 10] . ( 8 sec) [ -13945.6035] [ 2301] [depth= 1] . ( 8 sec) [ -13926.1940] [ 2299] [depth= 11] . ( 8 sec) [ -13902.2590] [ 2296] [depth= 1] . ( 8 sec) [ -13808.5370] [ 2291] [depth= 3] . ( 8 sec) [ -13663.5032] [ 2265] [depth= 10] . ( 8 sec) [ -13662.3664] [ 2266] [depth= 1] . ( 8 sec) [ -13614.3148] [ 2250] [depth= 7] . ( 8 sec) [ -13181.0825] [ 2244] [depth= 6] . ( 8 sec) [ -13059.3496] [ 2224] [depth= 1] . ( 8 sec) [ -12974.7618] [ 2219] [depth= 1] . ( 9 sec) [ -12969.3127] [ 2221] [depth= 1] . ( 9 sec) [ -12838.7362] [ 2215] [depth= 4] . ( 9 sec) [ -12758.0457] [ 2180] [depth= 4] . ( 9 sec) [ -12428.9483] [ 2164] [depth= 6] . ( 9 sec) [ -12386.7524] [ 2167] [depth= 4] . ( 9 sec) [ -12381.5275] [ 2165] [depth= 2] . ( 9 sec) [ -12356.1161] [ 2154] [depth= 4] . ( 9 sec) [ -12342.0060] [ 2156] [depth= 1] . ( 9 sec) [ -12188.8959] [ 2114] [depth= 10] . ( 10 sec) [ -12182.3938] [ 2113] [depth= 4] . ( 10 sec) [ -12130.6984] [ 2095] [depth= 3] . ( 10 sec) [ -12108.0375] [ 2091] [depth= 3] . ( 10 sec) [ -12077.8975] [ 2089] [depth= 3] . ( 10 sec) [ -12076.8798] [ 2092] [depth= 1] . ( 10 sec) [ -12070.9345] [ 2090] [depth= 2] . ( 10 sec) [ -12027.0065] [ 2076] [depth= 1] . ( 10 sec) [ -12014.5041] [ 2080] [depth= 1] . ( 10 sec) [ -12009.7347] [ 2079] [depth= 1] . ( 11 sec) [ -12001.1213] [ 2073] [depth= 5] . ( 11 sec) [ -11984.6975] [ 2075] [depth= 2] . ( 11 sec) [ -11976.0871] [ 2075] [depth= 2] . ( 11 sec) [ -11972.2233] [ 2072] [depth= 1] . ( 11 sec) [ -11926.7483] [ 2049] [depth= 3] . ( 11 sec) [ -11922.7439] [ 2066] [depth= 1] . ( 11 sec) [ -11834.2096] [ 2049] [depth= 1] . ( 11 sec) [ -11819.1898] [ 2049] [depth= 1] . ( 11 sec) [ -11785.0990] [ 2033] [depth= 1] . ( 11 sec) [ -11780.9332] [ 2033] [depth= 2] . ( 12 sec) [ -11727.4103] [ 2028] [depth= 1] . ( 12 sec) [ -11725.4756] [ 2027] [depth= 2] . ( 12 sec) [ -11702.0040] [ 2026] [depth= 8] . ( 12 sec) [ -11670.6544] [ 2018] [depth= 2] . ( 12 sec) [ -11670.3372] [ 2018] [depth= 2] . ( 12 sec) [ -11657.2678] [ 2006] [depth= 2] . ( 12 sec) [ -11650.9652] [ 2004] [depth= 2] . ( 12 sec) [ -11632.7608] [ 1995] [depth= 3] . ( 13 sec) [ -11630.0038] [ 1994] [depth= 4] . ( 14 sec) [ -11508.8254] [Branch lengths ] . ( 17 sec) [ -11264.2449] [GTR parameters ] . ( 17 sec) [ -11142.4163] [Alpha ][ 0.250961] . ( 18 sec) [ -11123.2392] [ 1981] [depth= 15] . ( 18 sec) [ -11122.9973] [ 1980] [depth= 1] . ( 19 sec) [ -11107.6321] [ 1971] [depth= 1] . ( 19 sec) [ -11070.4953] [ 1973] [depth= 1] . ( 19 sec) [ -11069.7612] [ 1970] [depth= 1] . ( 19 sec) [ -11064.2386] [ 1968] [depth= 1] . ( 21 sec) [ -11058.9522] [ 1982] [depth= 9] . ( 21 sec) [ -11041.7712] [ 1974] [depth= 5] . ( 21 sec) [ -11034.6564] [ 1971] [depth= 1] . ( 21 sec) [ -11030.4723] [ 1968] [depth= 1] . ( 22 sec) [ -11029.7321] [ 1968] [depth= 1] . ( 22 sec) [ -11027.4310] [ 1968] [depth= 1] . ( 23 sec) [ -11027.3477] [ 1969] [depth= 1] . ( 24 sec) [ -11026.6088] [ 1970] [depth= 1] . ( 24 sec) [ -10974.8448] [ 1937] [depth= 13] . ( 24 sec) [ -10973.6258] [ 1937] [depth= 1] . ( 25 sec) [ -10973.2443] [ 1938] [depth= 1] . ( 25 sec) [ -10972.9891] [ 1939] [depth= 1] . ( 27 sec) [ -10971.3038] [ 1938] [depth= 1] . ( 29 sec) [ -10969.6058] [ 1935] [depth= 1] . ( 29 sec) [ -10966.6408] [ 1939] [depth= 1] . ( 32 sec) [ -10951.2390] [Branch lengths ] . ( 35 sec) [ -10949.0256] [GTR parameters ] . ( 35 sec) [ -10946.0530] [Alpha ][ 0.222606] . ( 51 sec) [ -10944.2213] [Branch lengths ] . ( 109 sec) [ -10944.1220] [Branch lengths ] . ( 109 sec) [ -10944.1220] [Topology ] . ( 111 sec) [ -10944.1163] [Topology ] . ( 112 sec) [ -10944.1136] [Topology ] . ( 114 sec) [ -10944.1019] [Topology ] . ( 115 sec) [ -10944.0175] [Topology ] . ( 117 sec) [ -10943.4716] [Topology ] . ( 118 sec) [ -10941.5285] [Topology ] . ( 120 sec) [ -10941.4856] [GTR parameters ] . ( 120 sec) [ -10941.3674] [Alpha ][ 0.217371] . ( 120 sec) [ -10941.3674] [Topology ] . ( 122 sec) [ -10940.4278] [Topology ] . ( 123 sec) [ -10940.3077] [Topology ] . ( 125 sec) [ -10940.2803] [Topology ] . ( 126 sec) [ -10940.2709] [Topology ] . ( 127 sec) [ -10940.2672] [Topology ] . ( 129 sec) [ -10940.2657] [Topology ] . ( 129 sec) [ -10940.2657] [GTR parameters ] . ( 129 sec) [ -10940.2635] [Alpha ][ 0.216628] . ( 129 sec) [ -10940.2635] [Topology ] . ( 131 sec) [ -10940.2625] [Topology ] . ( 132 sec) [ -10940.2622] [Topology ] . ( 133 sec) [ -10940.2621] [GTR parameters ] . ( 133 sec) [ -10940.2621] [Alpha ][ 0.216628] . ( 133 sec) [ -10940.2621] [Topology ] . ( 134 sec) [ -10940.2620] [Topology ] . ( 136 sec) [ -10940.2596] [GTR parameters ] . ( 136 sec) [ -10940.2595] [Alpha ][ 0.216396] . ( 136 sec) [ -10940.2595] [Topology ] . ( 137 sec) [ -10940.2594] [Topology ] . ( 138 sec) [ -10940.2593] [GTR parameters ] . ( 138 sec) [ -10940.2593] [Alpha ][ 0.216396] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10940.259334. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21949.0306] [GTR parameters ] . ( 1 sec) [ -21348.2540] [Alpha ][ 0.500960] . ( 1 sec) [ -21065.8656] [ 3407] [depth= 8] . ( 1 sec) [ -20728.9806] [ 3343] [depth= 10] . ( 1 sec) [ -20704.6540] [ 3341] [depth= 1] . ( 1 sec) [ -20552.5564] [ 3335] [depth= 5] . ( 2 sec) [ -20499.4214] [ 3259] [depth= 2] . ( 2 sec) [ -20125.8786] [ 3251] [depth= 7] . ( 2 sec) [ -20018.8194] [ 3227] [depth= 6] . ( 2 sec) [ -19939.9245] [ 3224] [depth= 2] . ( 2 sec) [ -19778.2689] [ 3176] [depth= 1] . ( 2 sec) [ -19556.5188] [ 3169] [depth= 9] . ( 2 sec) [ -19401.8758] [ 3144] [depth= 2] . ( 2 sec) [ -19319.8184] [ 3126] [depth= 4] . ( 2 sec) [ -19139.8221] [ 3108] [depth= 13] . ( 2 sec) [ -19066.9032] [ 3087] [depth= 1] . ( 2 sec) [ -18765.4675] [ 3078] [depth= 6] . ( 2 sec) [ -18568.3058] [ 3026] [depth= 12] . ( 2 sec) [ -18536.3991] [ 3026] [depth= 1] . ( 3 sec) [ -18276.8968] [ 2987] [depth= 9] . ( 3 sec) [ -18241.6058] [ 2974] [depth= 11] . ( 3 sec) [ -18147.7212] [ 2964] [depth= 8] . ( 3 sec) [ -18022.4064] [ 2959] [depth= 1] . ( 3 sec) [ -17985.6358] [ 2948] [depth= 10] . ( 3 sec) [ -17960.8966] [ 2940] [depth= 1] . ( 3 sec) [ -17860.2940] [ 2931] [depth= 9] . ( 3 sec) [ -17839.1531] [ 2923] [depth= 1] . ( 3 sec) [ -17748.0994] [ 2899] [depth= 3] . ( 3 sec) [ -17743.6447] [ 2907] [depth= 10] . ( 3 sec) [ -17593.0449] [ 2901] [depth= 9] . ( 3 sec) [ -17522.8662] [ 2884] [depth= 1] . ( 4 sec) [ -17452.1350] [ 2853] [depth= 1] . ( 4 sec) [ -17222.1908] [ 2855] [depth= 1] . ( 4 sec) [ -17089.7604] [ 2815] [depth= 1] . ( 4 sec) [ -16932.4589] [ 2818] [depth= 2] . ( 4 sec) [ -16788.2095] [ 2807] [depth= 2] . ( 4 sec) [ -16641.0651] [ 2764] [depth= 3] . ( 4 sec) [ -16605.5119] [ 2758] [depth= 2] . ( 4 sec) [ -16449.4452] [ 2736] [depth= 13] . ( 4 sec) [ -16365.3026] [ 2732] [depth= 7] . ( 4 sec) [ -16233.6721] [ 2729] [depth= 8] . ( 4 sec) [ -16206.6445] [ 2703] [depth= 1] . ( 4 sec) [ -16114.6693] [ 2697] [depth= 10] . ( 5 sec) [ -16074.4593] [ 2708] [depth= 1] . ( 5 sec) [ -16058.9620] [ 2697] [depth= 1] . ( 5 sec) [ -16031.6339] [ 2691] [depth= 1] . ( 5 sec) [ -15811.7029] [ 2652] [depth= 10] . ( 5 sec) [ -15395.7580] [ 2642] [depth= 12] . ( 5 sec) [ -15323.3508] [ 2585] [depth= 9] . ( 5 sec) [ -15237.1071] [ 2573] [depth= 6] . ( 5 sec) [ -15236.5052] [ 2573] [depth= 1] . ( 5 sec) [ -15234.1439] [ 2573] [depth= 2] . ( 5 sec) [ -14939.2239] [ 2502] [depth= 5] . ( 5 sec) [ -14925.5597] [ 2495] [depth= 3] . ( 6 sec) [ -14811.5712] [ 2498] [depth= 4] . ( 6 sec) [ -14743.0823] [ 2467] [depth= 7] . ( 6 sec) [ -14662.1402] [ 2457] [depth= 2] . ( 6 sec) [ -14629.7587] [ 2448] [depth= 3] . ( 6 sec) [ -14408.6155] [ 2441] [depth= 3] . ( 6 sec) [ -14389.1246] [ 2439] [depth= 5] . ( 6 sec) [ -14389.0009] [ 2441] [depth= 1] . ( 6 sec) [ -14301.8980] [ 2418] [depth= 1] . ( 6 sec) [ -14148.0940] [ 2402] [depth= 13] . ( 6 sec) [ -14147.8323] [ 2395] [depth= 6] . ( 6 sec) [ -14136.4526] [ 2392] [depth= 8] . ( 6 sec) [ -13594.8688] [ 2328] [depth= 4] . ( 7 sec) [ -13522.0437] [ 2323] [depth= 1] . ( 7 sec) [ -13455.9164] [ 2300] [depth= 1] . ( 7 sec) [ -13412.7187] [ 2296] [depth= 6] . ( 7 sec) [ -13326.3917] [ 2258] [depth= 11] . ( 7 sec) [ -13287.1708] [ 2273] [depth= 1] . ( 7 sec) [ -13234.0828] [ 2270] [depth= 2] . ( 7 sec) [ -13190.8963] [ 2261] [depth= 6] . ( 7 sec) [ -13159.1588] [ 2254] [depth= 5] . ( 7 sec) [ -13133.9190] [ 2239] [depth= 1] . ( 7 sec) [ -13130.3685] [ 2237] [depth= 1] . ( 7 sec) [ -13011.4310] [ 2220] [depth= 2] . ( 8 sec) [ -12892.0087] [ 2214] [depth= 1] . ( 8 sec) [ -12888.7874] [ 2207] [depth= 6] . ( 8 sec) [ -12873.9033] [ 2208] [depth= 2] . ( 8 sec) [ -12870.4729] [ 2205] [depth= 1] . ( 8 sec) [ -12858.9663] [ 2203] [depth= 2] . ( 8 sec) [ -12785.4918] [ 2202] [depth= 1] . ( 8 sec) [ -12778.0970] [ 2202] [depth= 2] . ( 8 sec) [ -12769.5581] [ 2198] [depth= 3] . ( 8 sec) [ -12599.0844] [ 2196] [depth= 1] . ( 8 sec) [ -12311.7659] [ 2222] [depth= 1] . ( 8 sec) [ -12295.2168] [ 2217] [depth= 3] . ( 9 sec) [ -12269.3807] [ 2202] [depth= 10] . ( 9 sec) [ -12113.7755] [ 2227] [depth= 1] . ( 9 sec) [ -12028.1318] [ 2202] [depth= 1] . ( 9 sec) [ -11969.6225] [ 2193] [depth= 1] . ( 9 sec) [ -11940.4858] [ 2165] [depth= 12] . ( 9 sec) [ -11911.6667] [ 2162] [depth= 1] . ( 9 sec) [ -11860.9171] [ 2126] [depth= 8] . ( 9 sec) [ -11854.1698] [ 2122] [depth= 4] . ( 9 sec) [ -11839.6292] [ 2111] [depth= 1] . ( 9 sec) [ -11830.9656] [ 2110] [depth= 1] . ( 9 sec) [ -11809.4676] [ 2096] [depth= 5] . ( 9 sec) [ -11801.7617] [ 2094] [depth= 1] . ( 10 sec) [ -11698.8162] [ 2060] [depth= 1] . ( 10 sec) [ -11686.0589] [ 2057] [depth= 2] . ( 10 sec) [ -11686.0293] [ 2056] [depth= 1] . ( 10 sec) [ -11677.8074] [ 2055] [depth= 1] . ( 10 sec) [ -11671.1671] [ 2054] [depth= 2] . ( 10 sec) [ -11651.1418] [ 2057] [depth= 2] . ( 10 sec) [ -11630.4839] [ 2056] [depth= 1] . ( 10 sec) [ -11630.2533] [ 2049] [depth= 2] . ( 10 sec) [ -11627.2814] [ 2049] [depth= 2] . ( 10 sec) [ -11623.0041] [ 2049] [depth= 1] . ( 11 sec) [ -11622.8872] [ 2049] [depth= 1] . ( 11 sec) [ -11613.7710] [ 2043] [depth= 6] . ( 11 sec) [ -11610.6318] [ 2043] [depth= 1] . ( 11 sec) [ -11585.7777] [ 2041] [depth= 3] . ( 11 sec) [ -11549.3634] [ 2033] [depth= 6] . ( 11 sec) [ -11544.9469] [ 2038] [depth= 6] . ( 11 sec) [ -11539.6530] [ 2039] [depth= 2] . ( 11 sec) [ -11531.1866] [ 2037] [depth= 2] . ( 12 sec) [ -11497.3558] [ 2037] [depth= 1] . ( 12 sec) [ -11496.7387] [ 2039] [depth= 1] . ( 12 sec) [ -11495.9593] [ 2039] [depth= 3] . ( 12 sec) [ -11487.4650] [ 2040] [depth= 8] . ( 12 sec) [ -11487.4242] [ 2040] [depth= 1] . ( 13 sec) [ -11477.7211] [ 2031] [depth= 9] . ( 13 sec) [ -11475.6473] [ 2030] [depth= 1] . ( 13 sec) [ -11457.2033] [ 2029] [depth= 3] . ( 13 sec) [ -11452.4093] [ 2028] [depth= 1] . ( 14 sec) [ -11451.8809] [ 2028] [depth= 1] . ( 14 sec) [ -11421.3487] [ 2022] [depth= 3] . ( 14 sec) [ -11341.5166] [Branch lengths ] . ( 15 sec) [ -11263.0252] [GTR parameters ] . ( 15 sec) [ -11145.3076] [Alpha ][ 0.250961] . ( 16 sec) [ -11144.8515] [ 2020] [depth= 7] . ( 16 sec) [ -11123.9148] [ 2009] [depth= 1] . ( 16 sec) [ -11122.8913] [ 2007] [depth= 5] . ( 16 sec) [ -11119.6603] [ 2009] [depth= 2] . ( 17 sec) [ -11117.3257] [ 2006] [depth= 1] . ( 17 sec) [ -11117.1691] [ 2006] [depth= 1] . ( 17 sec) [ -11116.8630] [ 2006] [depth= 8] . ( 17 sec) [ -11092.5200] [ 1998] [depth= 1] . ( 17 sec) [ -11091.6414] [ 1997] [depth= 1] . ( 17 sec) [ -11089.5859] [ 1996] [depth= 3] . ( 18 sec) [ -11080.2603] [ 1990] [depth= 4] . ( 18 sec) [ -11078.7951] [ 1989] [depth= 1] . ( 18 sec) [ -11075.9319] [ 1989] [depth= 1] . ( 18 sec) [ -11071.3804] [ 1990] [depth= 1] . ( 19 sec) [ -11064.1811] [ 1988] [depth= 1] . ( 19 sec) [ -11060.6788] [ 1982] [depth= 2] . ( 19 sec) [ -11059.8229] [ 1987] [depth= 3] . ( 20 sec) [ -11056.5863] [ 1986] [depth= 1] . ( 20 sec) [ -11054.7390] [ 1986] [depth= 2] . ( 20 sec) [ -11047.6601] [ 1985] [depth= 6] . ( 21 sec) [ -11046.8879] [ 1982] [depth= 2] . ( 21 sec) [ -11046.5667] [ 1975] [depth= 1] . ( 21 sec) [ -11045.4644] [ 1974] [depth= 4] . ( 21 sec) [ -11041.4981] [ 1970] [depth= 1] . ( 22 sec) [ -11038.2323] [ 1969] [depth= 1] . ( 22 sec) [ -11038.1552] [ 1970] [depth= 3] . ( 23 sec) [ -11038.0873] [ 1969] [depth= 1] . ( 23 sec) [ -11035.8757] [ 1969] [depth= 1] . ( 23 sec) [ -11034.4183] [ 1963] [depth= 1] . ( 23 sec) [ -11032.5875] [ 1962] [depth= 1] . ( 23 sec) [ -11030.9122] [ 1961] [depth= 4] . ( 23 sec) [ -11027.3366] [ 1960] [depth= 6] . ( 23 sec) [ -11025.1395] [ 1958] [depth= 1] . ( 24 sec) [ -11015.6072] [ 1959] [depth= 1] . ( 24 sec) [ -11001.8357] [ 1948] [depth= 1] . ( 25 sec) [ -11001.6610] [ 1951] [depth= 1] . ( 25 sec) [ -10997.1884] [ 1948] [depth= 5] . ( 25 sec) [ -10996.5625] [ 1947] [depth= 1] . ( 26 sec) [ -10996.3099] [ 1948] [depth= 1] . ( 26 sec) [ -10990.9603] [ 1946] [depth= 2] . ( 27 sec) [ -10990.7154] [ 1945] [depth= 1] . ( 27 sec) [ -10987.8161] [ 1946] [depth= 1] . ( 28 sec) [ -10987.0069] [ 1946] [depth= 1] . ( 29 sec) [ -10970.3360] [Branch lengths ] . ( 30 sec) [ -10968.0306] [GTR parameters ] . ( 30 sec) [ -10965.5189] [Alpha ][ 0.224856] . ( 30 sec) [ -10964.5881] [ 1945] [depth= 1] . ( 31 sec) [ -10959.1842] [ 1943] [depth= 2] . ( 32 sec) [ -10958.9413] [ 1941] [depth= 1] . ( 33 sec) [ -10957.7036] [ 1940] [depth= 1] . ( 38 sec) [ -10953.0955] [ 1941] [depth= 4] . ( 38 sec) [ -10952.9272] [ 1940] [depth= 1] . ( 39 sec) [ -10951.8635] [ 1939] [depth= 1] . ( 43 sec) [ -10950.5517] [ 1939] [depth= 1] . ( 44 sec) [ -10950.4841] [ 1940] [depth= 1] . ( 46 sec) [ -10943.7145] [Branch lengths ] . ( 46 sec) [ -10943.6449] [GTR parameters ] . ( 46 sec) [ -10943.4616] [Alpha ][ 0.218249] . ( 63 sec) [ -10943.1898] [Branch lengths ] . ( 122 sec) [ -10943.1746] [Branch lengths ] . ( 122 sec) [ -10943.1746] [Topology ] . ( 123 sec) [ -10943.1719] [Topology ] . ( 125 sec) [ -10943.1577] [Topology ] . ( 126 sec) [ -10943.0527] [Topology ] . ( 127 sec) [ -10942.3970] [Topology ] . ( 129 sec) [ -10940.3207] [Topology ] . ( 130 sec) [ -10939.6455] [Topology ] . ( 131 sec) [ -10939.6445] [GTR parameters ] . ( 131 sec) [ -10939.6306] [Alpha ][ 0.216379] . ( 131 sec) [ -10939.6306] [Topology ] . ( 132 sec) [ -10939.5380] [Topology ] . ( 134 sec) [ -10939.5146] [Topology ] . ( 135 sec) [ -10939.5064] [Topology ] . ( 137 sec) [ -10939.5031] [Topology ] . ( 138 sec) [ -10939.5017] [Topology ] . ( 139 sec) [ -10939.5012] [Topology ] . ( 140 sec) [ -10939.5009] [GTR parameters ] . ( 140 sec) [ -10939.5005] [Alpha ][ 0.216040] . ( 140 sec) [ -10939.5005] [Topology ] . ( 142 sec) [ -10939.5002] [Topology ] . ( 142 sec) [ -10939.5002] [GTR parameters ] . ( 142 sec) [ -10939.5002] [Alpha ][ 0.216040] . Checking for NNIs, optimizing five branches... . ( 152 sec) [ -10939.3343] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10939.334301. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22468.2964] [GTR parameters ] . ( 2 sec) [ -21892.1602] [Alpha ][ 0.500960] . ( 2 sec) [ -21621.3700] [ 3430] [depth= 8] . ( 2 sec) [ -21436.7268] [ 3366] [depth= 11] . ( 2 sec) [ -21245.1544] [ 3364] [depth= 2] . ( 2 sec) [ -21214.8257] [ 3360] [depth= 9] . ( 3 sec) [ -21198.8143] [ 3348] [depth= 3] . ( 3 sec) [ -21138.0110] [ 3346] [depth= 3] . ( 3 sec) [ -21128.1669] [ 3348] [depth= 1] . ( 3 sec) [ -21102.5779] [ 3348] [depth= 10] . ( 3 sec) [ -20917.1292] [ 3331] [depth= 6] . ( 3 sec) [ -20847.4125] [ 3329] [depth= 6] . ( 3 sec) [ -20736.3516] [ 3331] [depth= 1] . ( 3 sec) [ -20596.8020] [ 3307] [depth= 13] . ( 3 sec) [ -20564.2470] [ 3289] [depth= 2] . ( 3 sec) [ -20481.3502] [ 3284] [depth= 14] . ( 3 sec) [ -20345.4849] [ 3263] [depth= 2] . ( 3 sec) [ -20305.4232] [ 3249] [depth= 8] . ( 3 sec) [ -20292.6407] [ 3245] [depth= 9] . ( 4 sec) [ -20265.7354] [ 3242] [depth= 2] . ( 4 sec) [ -20162.5318] [ 3238] [depth= 14] . ( 4 sec) [ -20132.1595] [ 3237] [depth= 1] . ( 4 sec) [ -19963.4536] [ 3174] [depth= 15] . ( 4 sec) [ -19638.4902] [ 3170] [depth= 10] . ( 4 sec) [ -19421.2926] [ 3166] [depth= 6] . ( 4 sec) [ -19289.5427] [ 3157] [depth= 1] . ( 4 sec) [ -18865.0710] [ 3134] [depth= 1] . ( 4 sec) [ -18660.3282] [ 3086] [depth= 10] . ( 4 sec) [ -18644.4484] [ 3084] [depth= 15] . ( 4 sec) [ -18639.4433] [ 3082] [depth= 1] . ( 4 sec) [ -18612.9170] [ 3081] [depth= 1] . ( 5 sec) [ -18584.3255] [ 3074] [depth= 5] . ( 5 sec) [ -18510.9106] [ 3055] [depth= 1] . ( 5 sec) [ -18321.7714] [ 3028] [depth= 7] . ( 5 sec) [ -18125.9642] [ 2981] [depth= 2] . ( 5 sec) [ -18066.1663] [ 2981] [depth= 2] . ( 5 sec) [ -17980.5618] [ 2981] [depth= 2] . ( 5 sec) [ -17906.5915] [ 2973] [depth= 6] . ( 5 sec) [ -17877.3369] [ 2950] [depth= 1] . ( 5 sec) [ -17870.2189] [ 2945] [depth= 2] . ( 5 sec) [ -17810.6835] [ 2934] [depth= 1] . ( 5 sec) [ -17710.5794] [ 2934] [depth= 3] . ( 5 sec) [ -17616.7333] [ 2877] [depth= 6] . ( 6 sec) [ -17607.7980] [ 2877] [depth= 2] . ( 6 sec) [ -17603.4733] [ 2877] [depth= 2] . ( 6 sec) [ -17601.9480] [ 2877] [depth= 1] . ( 6 sec) [ -17265.6148] [ 2880] [depth= 7] . ( 6 sec) [ -17242.1936] [ 2880] [depth= 1] . ( 6 sec) [ -17019.6267] [ 2807] [depth= 4] . ( 6 sec) [ -16920.3011] [ 2802] [depth= 9] . ( 6 sec) [ -16875.9569] [ 2767] [depth= 5] . ( 6 sec) [ -16838.6315] [ 2765] [depth= 6] . ( 6 sec) [ -16699.1021] [ 2754] [depth= 1] . ( 6 sec) [ -16521.1686] [ 2752] [depth= 2] . ( 6 sec) [ -15895.0693] [ 2689] [depth= 13] . ( 7 sec) [ -15876.9537] [ 2678] [depth= 2] . ( 7 sec) [ -15621.4391] [ 2611] [depth= 12] . ( 7 sec) [ -15494.4392] [ 2586] [depth= 12] . ( 7 sec) [ -15452.4468] [ 2579] [depth= 6] . ( 7 sec) [ -15301.7464] [ 2553] [depth= 2] . ( 7 sec) [ -15281.1378] [ 2542] [depth= 7] . ( 7 sec) [ -15177.3542] [ 2541] [depth= 1] . ( 7 sec) [ -15142.3678] [ 2522] [depth= 2] . ( 7 sec) [ -15142.3548] [ 2525] [depth= 1] . ( 7 sec) [ -15075.9558] [ 2520] [depth= 9] . ( 7 sec) [ -14914.6938] [ 2518] [depth= 2] . ( 7 sec) [ -14877.5914] [ 2505] [depth= 2] . ( 8 sec) [ -14620.0055] [ 2495] [depth= 14] . ( 8 sec) [ -14460.8911] [ 2475] [depth= 4] . ( 8 sec) [ -14436.0135] [ 2464] [depth= 8] . ( 8 sec) [ -14418.1031] [ 2456] [depth= 2] . ( 8 sec) [ -14382.9598] [ 2450] [depth= 2] . ( 8 sec) [ -14089.3220] [ 2445] [depth= 5] . ( 8 sec) [ -13787.9270] [ 2426] [depth= 9] . ( 8 sec) [ -13756.2428] [ 2407] [depth= 3] . ( 8 sec) [ -13722.5101] [ 2402] [depth= 1] . ( 9 sec) [ -13711.0532] [ 2402] [depth= 6] . ( 9 sec) [ -13591.3049] [ 2385] [depth= 12] . ( 9 sec) [ -13578.7469] [ 2383] [depth= 1] . ( 9 sec) [ -13575.7960] [ 2381] [depth= 2] . ( 9 sec) [ -13568.9567] [ 2381] [depth= 2] . ( 9 sec) [ -13390.2475] [ 2334] [depth= 10] . ( 9 sec) [ -13389.6752] [ 2335] [depth= 1] . ( 9 sec) [ -13252.1826] [ 2287] [depth= 9] . ( 9 sec) [ -13239.5037] [ 2283] [depth= 1] . ( 9 sec) [ -13177.9937] [ 2276] [depth= 10] . ( 10 sec) [ -13044.8346] [ 2250] [depth= 5] . ( 10 sec) [ -13010.8786] [ 2231] [depth= 8] . ( 10 sec) [ -12782.6431] [ 2166] [depth= 2] . ( 10 sec) [ -12707.2930] [ 2163] [depth= 1] . ( 10 sec) [ -12694.2184] [ 2157] [depth= 1] . ( 10 sec) [ -12660.2430] [ 2149] [depth= 4] . ( 10 sec) [ -12617.3286] [ 2142] [depth= 5] . ( 10 sec) [ -12534.8651] [ 2142] [depth= 1] . ( 10 sec) [ -12365.3416] [ 2134] [depth= 4] . ( 10 sec) [ -12350.7380] [ 2127] [depth= 1] . ( 11 sec) [ -12307.1313] [ 2125] [depth= 6] . ( 11 sec) [ -12303.0228] [ 2121] [depth= 1] . ( 11 sec) [ -12276.9787] [ 2112] [depth= 14] . ( 11 sec) [ -12237.9033] [ 2107] [depth= 6] . ( 11 sec) [ -12181.9876] [ 2112] [depth= 7] . ( 11 sec) [ -12179.0730] [ 2102] [depth= 7] . ( 11 sec) [ -12146.6056] [ 2078] [depth= 1] . ( 11 sec) [ -12077.8232] [ 2078] [depth= 2] . ( 11 sec) [ -12041.1135] [ 2079] [depth= 1] . ( 11 sec) [ -11977.5653] [ 2083] [depth= 14] . ( 12 sec) [ -11917.8742] [ 2065] [depth= 16] . ( 12 sec) [ -11870.8891] [ 2078] [depth= 1] . ( 12 sec) [ -11869.6452] [ 2081] [depth= 1] . ( 12 sec) [ -11831.5845] [ 2078] [depth= 3] . ( 12 sec) [ -11830.4502] [ 2075] [depth= 4] . ( 12 sec) [ -11829.1900] [ 2074] [depth= 1] . ( 12 sec) [ -11791.6552] [ 2065] [depth= 1] . ( 12 sec) [ -11774.1986] [ 2062] [depth= 2] . ( 12 sec) [ -11736.7344] [ 2064] [depth= 2] . ( 12 sec) [ -11608.3195] [ 2054] [depth= 4] . ( 13 sec) [ -11605.4746] [ 2021] [depth= 2] . ( 13 sec) [ -11585.3281] [ 2024] [depth= 1] . ( 13 sec) [ -11576.1969] [ 2023] [depth= 1] . ( 13 sec) [ -11565.6994] [ 2021] [depth= 1] . ( 13 sec) [ -11562.9174] [ 2021] [depth= 2] . ( 13 sec) [ -11534.6289] [ 2026] [depth= 1] . ( 13 sec) [ -11514.4835] [ 2012] [depth= 1] . ( 13 sec) [ -11471.7523] [ 2013] [depth= 1] . ( 13 sec) [ -11471.7267] [ 2014] [depth= 1] . ( 13 sec) [ -11469.3140] [ 2011] [depth= 1] . ( 13 sec) [ -11464.0530] [ 2013] [depth= 2] . ( 14 sec) [ -11463.4577] [ 2013] [depth= 1] . ( 14 sec) [ -11460.6253] [ 2012] [depth= 1] . ( 14 sec) [ -11454.6509] [ 2010] [depth= 1] . ( 14 sec) [ -11448.3921] [ 2011] [depth= 4] . ( 15 sec) [ -11358.7611] [Branch lengths ] . ( 18 sec) [ -11254.5348] [GTR parameters ] . ( 18 sec) [ -11130.3162] [Alpha ][ 0.250961] . ( 18 sec) [ -11118.8057] [ 2009] [depth= 1] . ( 18 sec) [ -11118.7540] [ 2012] [depth= 1] . ( 18 sec) [ -11111.7903] [ 2011] [depth= 2] . ( 18 sec) [ -11108.8226] [ 2010] [depth= 1] . ( 19 sec) [ -11062.1001] [ 1986] [depth= 12] . ( 19 sec) [ -11057.8551] [ 1983] [depth= 1] . ( 19 sec) [ -11050.2444] [ 1974] [depth= 8] . ( 19 sec) [ -11048.4471] [ 1974] [depth= 1] . ( 19 sec) [ -11045.8605] [ 1974] [depth= 1] . ( 19 sec) [ -11035.6602] [ 1970] [depth= 2] . ( 19 sec) [ -11034.2457] [ 1969] [depth= 1] . ( 20 sec) [ -11030.1971] [ 1967] [depth= 5] . ( 20 sec) [ -11024.4387] [ 1964] [depth= 1] . ( 20 sec) [ -11019.4408] [ 1960] [depth= 2] . ( 21 sec) [ -11019.4280] [ 1960] [depth= 2] . ( 21 sec) [ -11017.9877] [ 1961] [depth= 1] . ( 21 sec) [ -11017.9500] [ 1962] [depth= 2] . ( 22 sec) [ -11009.3659] [ 1957] [depth= 3] . ( 22 sec) [ -11003.1149] [ 1950] [depth= 7] . ( 22 sec) [ -10999.1280] [ 1948] [depth= 1] . ( 23 sec) [ -10995.3031] [ 1946] [depth= 1] . ( 24 sec) [ -10984.9593] [ 1942] [depth= 1] . ( 24 sec) [ -10984.1899] [ 1945] [depth= 1] . ( 25 sec) [ -10983.5620] [ 1946] [depth= 1] . ( 25 sec) [ -10981.5270] [ 1944] [depth= 1] . ( 25 sec) [ -10981.3536] [ 1943] [depth= 1] . ( 25 sec) [ -10980.7725] [ 1944] [depth= 1] . ( 26 sec) [ -10979.7183] [ 1949] [depth= 1] . ( 27 sec) [ -10976.5505] [ 1944] [depth= 1] . ( 27 sec) [ -10976.4071] [ 1944] [depth= 1] . ( 28 sec) [ -10975.3005] [ 1947] [depth= 1] . ( 28 sec) [ -10974.8055] [ 1947] [depth= 1] . ( 30 sec) [ -10973.4146] [ 1947] [depth= 1] . ( 30 sec) [ -10973.3738] [ 1949] [depth= 1] . ( 30 sec) [ -10971.7091] [ 1949] [depth= 1] . ( 31 sec) [ -10971.4832] [ 1946] [depth= 1] . ( 31 sec) [ -10969.1334] [ 1944] [depth= 1] . ( 32 sec) [ -10968.1646] [ 1943] [depth= 2] . ( 33 sec) [ -10956.5240] [Branch lengths ] . ( 36 sec) [ -10952.7038] [GTR parameters ] . ( 36 sec) [ -10948.9908] [Alpha ][ 0.219342] . ( 37 sec) [ -10948.6690] [ 1941] [depth= 1] . ( 52 sec) [ -10947.6711] [Branch lengths ] . ( 54 sec) [ -10947.5624] [GTR parameters ] . ( 54 sec) [ -10947.5362] [Alpha ][ 0.216799] . ( 70 sec) [ -10946.1569] [Branch lengths ] . ( 112 sec) [ -10946.0456] [ 1940] [depth= 1] . ( 128 sec) [ -10941.6520] [Branch lengths ] . ( 130 sec) [ -10941.6488] [GTR parameters ] . ( 130 sec) [ -10941.6485] [Alpha ][ 0.216520] . ( 189 sec) [ -10940.6652] [Branch lengths ] . ( 189 sec) [ -10940.6652] [Topology ] . ( 191 sec) [ -10940.1752] [Topology ] . ( 192 sec) [ -10939.7715] [Topology ] . ( 193 sec) [ -10939.7253] [Topology ] . ( 195 sec) [ -10939.7140] [Topology ] . ( 196 sec) [ -10939.7109] [Topology ] . ( 198 sec) [ -10939.7100] [Topology ] . ( 199 sec) [ -10939.7084] [GTR parameters ] . ( 199 sec) [ -10939.7055] [Alpha ][ 0.215648] . ( 199 sec) [ -10939.7055] [Topology ] . ( 201 sec) [ -10939.7043] [Topology ] . ( 202 sec) [ -10939.7039] [Topology ] . ( 202 sec) [ -10939.7039] [GTR parameters ] . ( 202 sec) [ -10939.7038] [Alpha ][ 0.215432] . ( 203 sec) [ -10939.7038] [Topology ] . ( 204 sec) [ -10939.7035] [Topology ] . ( 204 sec) [ -10939.7035] [GTR parameters ] . ( 204 sec) [ -10939.7035] [Alpha ][ 0.215432] . Checking for NNIs, optimizing five branches... . ( 215 sec) [ -10939.5140] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10939.514005. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23457.7857] [GTR parameters ] . ( 1 sec) [ -22892.3693] [Alpha ][ 0.500960] . ( 1 sec) [ -21463.6781] [ 3450] [depth= 10] . ( 1 sec) [ -21239.4293] [ 3373] [depth= 5] . ( 2 sec) [ -21069.1927] [ 3337] [depth= 9] . ( 2 sec) [ -21037.9373] [ 3291] [depth= 1] . ( 2 sec) [ -20746.4978] [ 3249] [depth= 8] . ( 2 sec) [ -20685.0677] [ 3244] [depth= 5] . ( 2 sec) [ -20601.8959] [ 3243] [depth= 1] . ( 2 sec) [ -20443.8740] [ 3233] [depth= 5] . ( 2 sec) [ -20440.6092] [ 3232] [depth= 5] . ( 2 sec) [ -20354.5395] [ 3209] [depth= 1] . ( 2 sec) [ -20300.5174] [ 3205] [depth= 4] . ( 2 sec) [ -20205.9476] [ 3197] [depth= 6] . ( 2 sec) [ -19857.0897] [ 3114] [depth= 13] . ( 2 sec) [ -19696.4444] [ 3077] [depth= 13] . ( 3 sec) [ -19572.0393] [ 3077] [depth= 3] . ( 3 sec) [ -19553.5448] [ 3075] [depth= 1] . ( 3 sec) [ -19327.9853] [ 3072] [depth= 1] . ( 3 sec) [ -19029.3251] [ 3052] [depth= 8] . ( 3 sec) [ -18828.2149] [ 3043] [depth= 3] . ( 3 sec) [ -18821.5866] [ 3042] [depth= 1] . ( 3 sec) [ -18807.8045] [ 3036] [depth= 2] . ( 3 sec) [ -18756.9020] [ 3036] [depth= 2] . ( 3 sec) [ -18665.9497] [ 3018] [depth= 1] . ( 3 sec) [ -18318.6388] [ 3012] [depth= 4] . ( 3 sec) [ -18317.4552] [ 3012] [depth= 3] . ( 3 sec) [ -17983.9569] [ 2944] [depth= 14] . ( 3 sec) [ -17959.3461] [ 2937] [depth= 1] . ( 4 sec) [ -17938.0579] [ 2927] [depth= 4] . ( 4 sec) [ -17909.6065] [ 2924] [depth= 1] . ( 4 sec) [ -17338.5247] [ 2894] [depth= 6] . ( 4 sec) [ -17286.5059] [ 2886] [depth= 1] . ( 4 sec) [ -17219.9170] [ 2851] [depth= 15] . ( 4 sec) [ -16792.9206] [ 2807] [depth= 1] . ( 4 sec) [ -16705.7022] [ 2782] [depth= 15] . ( 4 sec) [ -16503.9701] [ 2739] [depth= 7] . ( 4 sec) [ -16493.9679] [ 2778] [depth= 4] . ( 4 sec) [ -16415.2323] [ 2762] [depth= 6] . ( 4 sec) [ -15964.1487] [ 2753] [depth= 13] . ( 4 sec) [ -15953.7492] [ 2750] [depth= 1] . ( 5 sec) [ -15929.9189] [ 2727] [depth= 6] . ( 5 sec) [ -15898.0901] [ 2723] [depth= 1] . ( 5 sec) [ -15587.6887] [ 2658] [depth= 18] . ( 5 sec) [ -15499.9922] [ 2620] [depth= 1] . ( 5 sec) [ -15440.1762] [ 2609] [depth= 2] . ( 5 sec) [ -15338.8503] [ 2597] [depth= 7] . ( 5 sec) [ -15321.5331] [ 2593] [depth= 1] . ( 5 sec) [ -15212.2620] [ 2570] [depth= 13] . ( 5 sec) [ -15191.7551] [ 2568] [depth= 2] . ( 5 sec) [ -15085.3511] [ 2551] [depth= 18] . ( 5 sec) [ -15056.6694] [ 2551] [depth= 1] . ( 5 sec) [ -15053.4581] [ 2553] [depth= 1] . ( 6 sec) [ -14955.2722] [ 2535] [depth= 5] . ( 6 sec) [ -14920.5968] [ 2540] [depth= 1] . ( 6 sec) [ -14823.8575] [ 2529] [depth= 3] . ( 6 sec) [ -14644.1780] [ 2497] [depth= 2] . ( 6 sec) [ -14635.7860] [ 2492] [depth= 1] . ( 6 sec) [ -14605.7464] [ 2495] [depth= 3] . ( 6 sec) [ -14446.8192] [ 2486] [depth= 6] . ( 6 sec) [ -14306.1620] [ 2458] [depth= 1] . ( 6 sec) [ -14227.5631] [ 2450] [depth= 8] . ( 6 sec) [ -14205.7540] [ 2438] [depth= 1] . ( 6 sec) [ -14089.1410] [ 2415] [depth= 7] . ( 7 sec) [ -13923.5305] [ 2388] [depth= 1] . ( 7 sec) [ -13891.8033] [ 2380] [depth= 10] . ( 7 sec) [ -13876.7377] [ 2381] [depth= 1] . ( 7 sec) [ -13857.6130] [ 2381] [depth= 1] . ( 7 sec) [ -13755.6717] [ 2378] [depth= 3] . ( 7 sec) [ -13749.2597] [ 2373] [depth= 3] . ( 7 sec) [ -13675.2314] [ 2372] [depth= 12] . ( 7 sec) [ -13654.4703] [ 2362] [depth= 2] . ( 7 sec) [ -13621.7773] [ 2358] [depth= 3] . ( 7 sec) [ -13619.7284] [ 2359] [depth= 1] . ( 7 sec) [ -13600.9167] [ 2359] [depth= 1] . ( 8 sec) [ -13287.8215] [ 2306] [depth= 8] . ( 8 sec) [ -13151.3212] [ 2306] [depth= 2] . ( 8 sec) [ -13151.2309] [ 2306] [depth= 2] . ( 8 sec) [ -13129.0678] [ 2300] [depth= 2] . ( 8 sec) [ -13105.3101] [ 2303] [depth= 5] . ( 8 sec) [ -13096.6950] [ 2297] [depth= 4] . ( 8 sec) [ -13009.6383] [ 2287] [depth= 3] . ( 8 sec) [ -12962.7637] [ 2271] [depth= 1] . ( 8 sec) [ -12959.9697] [ 2268] [depth= 2] . ( 9 sec) [ -12889.1110] [ 2240] [depth= 11] . ( 9 sec) [ -12871.6800] [ 2238] [depth= 1] . ( 9 sec) [ -12839.7451] [ 2221] [depth= 13] . ( 9 sec) [ -12834.9369] [ 2223] [depth= 1] . ( 9 sec) [ -12828.2013] [ 2223] [depth= 2] . ( 9 sec) [ -12636.6361] [ 2180] [depth= 11] . ( 9 sec) [ -12615.7717] [ 2171] [depth= 1] . ( 9 sec) [ -12578.9023] [ 2172] [depth= 7] . ( 9 sec) [ -12565.5936] [ 2150] [depth= 13] . ( 9 sec) [ -12547.9234] [ 2160] [depth= 6] . ( 9 sec) [ -12540.2397] [ 2148] [depth= 8] . ( 10 sec) [ -12540.0740] [ 2149] [depth= 1] . ( 10 sec) [ -12536.8382] [ 2149] [depth= 3] . ( 10 sec) [ -12466.6747] [ 2147] [depth= 1] . ( 10 sec) [ -12417.9712] [ 2134] [depth= 4] . ( 10 sec) [ -12374.9639] [ 2132] [depth= 1] . ( 10 sec) [ -12346.1842] [ 2128] [depth= 3] . ( 10 sec) [ -12339.7521] [ 2129] [depth= 3] . ( 10 sec) [ -12336.3438] [ 2123] [depth= 3] . ( 10 sec) [ -12312.1799] [ 2118] [depth= 4] . ( 10 sec) [ -12287.8262] [ 2117] [depth= 1] . ( 10 sec) [ -12284.3407] [ 2117] [depth= 1] . ( 10 sec) [ -12271.8620] [ 2115] [depth= 2] . ( 11 sec) [ -12268.7732] [ 2116] [depth= 1] . ( 11 sec) [ -12267.7097] [ 2133] [depth= 1] . ( 11 sec) [ -12244.2835] [ 2116] [depth= 1] . ( 11 sec) [ -12201.6883] [ 2085] [depth= 12] . ( 11 sec) [ -12178.8748] [ 2083] [depth= 5] . ( 11 sec) [ -12166.3061] [ 2078] [depth= 1] . ( 11 sec) [ -12163.4822] [ 2087] [depth= 1] . ( 11 sec) [ -12149.8027] [ 2079] [depth= 5] . ( 12 sec) [ -12149.1634] [ 2081] [depth= 1] . ( 12 sec) [ -12148.7111] [ 2080] [depth= 8] . ( 12 sec) [ -11935.2791] [ 2072] [depth= 1] . ( 12 sec) [ -11923.6656] [ 2066] [depth= 10] . ( 13 sec) [ -11892.0965] [ 2061] [depth= 4] . ( 13 sec) [ -11889.1936] [ 2062] [depth= 2] . ( 13 sec) [ -11885.5574] [ 2063] [depth= 1] . ( 13 sec) [ -11884.8715] [ 2065] [depth= 1] . ( 13 sec) [ -11856.8926] [ 2050] [depth= 11] . ( 13 sec) [ -11837.9558] [ 2040] [depth= 4] . ( 13 sec) [ -11795.6929] [ 2043] [depth= 1] . ( 13 sec) [ -11760.3342] [ 2036] [depth= 3] . ( 13 sec) [ -11719.3264] [ 2026] [depth= 1] . ( 13 sec) [ -11719.2959] [ 2026] [depth= 1] . ( 14 sec) [ -11624.2439] [Branch lengths ] . ( 18 sec) [ -11312.6789] [GTR parameters ] . ( 18 sec) [ -11193.3799] [Alpha ][ 0.250961] . ( 18 sec) [ -11148.3009] [ 2008] [depth= 8] . ( 19 sec) [ -11146.6515] [ 2006] [depth= 1] . ( 19 sec) [ -11146.3826] [ 2007] [depth= 1] . ( 19 sec) [ -11134.4146] [ 2005] [depth= 3] . ( 20 sec) [ -11130.7208] [ 2002] [depth= 2] . ( 20 sec) [ -11130.6424] [ 2004] [depth= 1] . ( 20 sec) [ -11128.5493] [ 2003] [depth= 3] . ( 21 sec) [ -11118.0071] [ 1996] [depth= 3] . ( 21 sec) [ -11095.7162] [ 1986] [depth= 6] . ( 21 sec) [ -11092.4337] [ 1986] [depth= 1] . ( 22 sec) [ -11086.1009] [ 1983] [depth= 2] . ( 22 sec) [ -11085.3014] [ 1985] [depth= 1] . ( 22 sec) [ -11081.4891] [ 1982] [depth= 2] . ( 23 sec) [ -11073.4925] [ 1981] [depth= 1] . ( 23 sec) [ -11048.1912] [ 1972] [depth= 1] . ( 23 sec) [ -11045.1298] [ 1966] [depth= 1] . ( 23 sec) [ -11035.8382] [ 1965] [depth= 4] . ( 23 sec) [ -11029.0727] [ 1964] [depth= 4] . ( 23 sec) [ -11027.6788] [ 1961] [depth= 3] . ( 23 sec) [ -11027.4617] [ 1961] [depth= 2] . ( 24 sec) [ -11026.5669] [ 1963] [depth= 1] . ( 25 sec) [ -11026.5525] [ 1963] [depth= 2] . ( 25 sec) [ -11025.6329] [ 1961] [depth= 1] . ( 26 sec) [ -11025.5038] [ 1963] [depth= 2] . ( 26 sec) [ -11025.3752] [ 1958] [depth= 3] . ( 26 sec) [ -11022.8136] [ 1957] [depth= 2] . ( 26 sec) [ -11018.3531] [ 1959] [depth= 1] . ( 27 sec) [ -11016.3893] [ 1963] [depth= 1] . ( 27 sec) [ -11012.2872] [ 1959] [depth= 1] . ( 27 sec) [ -10997.2290] [ 1945] [depth= 3] . ( 27 sec) [ -10994.7108] [ 1946] [depth= 1] . ( 28 sec) [ -10990.3779] [ 1949] [depth= 1] . ( 28 sec) [ -10986.5089] [ 1948] [depth= 2] . ( 28 sec) [ -10986.3050] [ 1949] [depth= 1] . ( 29 sec) [ -10983.5232] [ 1950] [depth= 1] . ( 29 sec) [ -10982.2364] [ 1947] [depth= 1] . ( 30 sec) [ -10981.4373] [ 1948] [depth= 1] . ( 31 sec) [ -10977.9593] [ 1943] [depth= 1] . ( 32 sec) [ -10960.8076] [Branch lengths ] . ( 36 sec) [ -10952.8809] [GTR parameters ] . ( 36 sec) [ -10950.0211] [Alpha ][ 0.223323] . ( 37 sec) [ -10949.3114] [ 1944] [depth= 1] . ( 38 sec) [ -10949.0408] [ 1943] [depth= 1] . ( 40 sec) [ -10948.4404] [ 1941] [depth= 1] . ( 45 sec) [ -10948.3902] [ 1941] [depth= 2] . ( 46 sec) [ -10947.7542] [ 1941] [depth= 1] . ( 49 sec) [ -10947.6298] [ 1939] [depth= 3] . ( 51 sec) [ -10942.9864] [Branch lengths ] . ( 54 sec) [ -10942.9291] [GTR parameters ] . ( 54 sec) [ -10942.8209] [Alpha ][ 0.218326] . ( 70 sec) [ -10942.4375] [Branch lengths ] . ( 129 sec) [ -10942.4225] [Branch lengths ] . ( 129 sec) [ -10942.4225] [Topology ] . ( 130 sec) [ -10942.4085] [Topology ] . ( 132 sec) [ -10942.3090] [Topology ] . ( 133 sec) [ -10941.7292] [Topology ] . ( 134 sec) [ -10940.7158] [Topology ] . ( 136 sec) [ -10940.5612] [Topology ] . ( 137 sec) [ -10940.5367] [Topology ] . ( 138 sec) [ -10940.5367] [GTR parameters ] . ( 138 sec) [ -10940.5222] [Alpha ][ 0.216422] . ( 138 sec) [ -10940.5222] [Topology ] . ( 139 sec) [ -10940.5148] [Topology ] . ( 141 sec) [ -10940.5129] [Topology ] . ( 142 sec) [ -10940.5123] [Topology ] . ( 144 sec) [ -10940.5098] [GTR parameters ] . ( 144 sec) [ -10940.5094] [Alpha ][ 0.216064] . ( 144 sec) [ -10940.5094] [Topology ] . ( 146 sec) [ -10940.5089] [Topology ] . ( 146 sec) [ -10940.5088] [GTR parameters ] . ( 146 sec) [ -10940.5088] [Alpha ][ 0.216064] . Checking for NNIs, optimizing five branches... . ( 157 sec) [ -10940.4658] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10940.465830. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24060.3848] [GTR parameters ] . ( 1 sec) [ -23451.6004] [Alpha ][ 0.500960] . ( 1 sec) [ -22564.9645] [ 3459] [depth= 6] . ( 1 sec) [ -22296.3247] [ 3415] [depth= 10] . ( 2 sec) [ -22209.7776] [ 3413] [depth= 3] . ( 2 sec) [ -22200.0143] [ 3411] [depth= 2] . ( 2 sec) [ -22172.0040] [ 3393] [depth= 4] . ( 2 sec) [ -22105.7347] [ 3390] [depth= 2] . ( 2 sec) [ -22061.4120] [ 3383] [depth= 8] . ( 2 sec) [ -21879.1438] [ 3354] [depth= 10] . ( 2 sec) [ -21698.4624] [ 3320] [depth= 10] . ( 2 sec) [ -21455.5698] [ 3286] [depth= 8] . ( 2 sec) [ -21259.5915] [ 3301] [depth= 6] . ( 2 sec) [ -21117.9761] [ 3290] [depth= 6] . ( 2 sec) [ -20839.4813] [ 3216] [depth= 10] . ( 2 sec) [ -20573.5851] [ 3194] [depth= 14] . ( 3 sec) [ -20375.2909] [ 3194] [depth= 2] . ( 3 sec) [ -19747.2717] [ 3223] [depth= 9] . ( 3 sec) [ -19595.7887] [ 3204] [depth= 6] . ( 3 sec) [ -19541.1205] [ 3204] [depth= 3] . ( 3 sec) [ -19379.2501] [ 3154] [depth= 11] . ( 3 sec) [ -19319.8711] [ 3149] [depth= 2] . ( 3 sec) [ -19147.2532] [ 3105] [depth= 14] . ( 3 sec) [ -18434.1596] [ 3068] [depth= 8] . ( 3 sec) [ -18403.2960] [ 3036] [depth= 10] . ( 3 sec) [ -18218.2095] [ 3038] [depth= 1] . ( 3 sec) [ -18034.6245] [ 3020] [depth= 5] . ( 3 sec) [ -17605.0175] [ 2930] [depth= 6] . ( 4 sec) [ -17547.6888] [ 2909] [depth= 1] . ( 4 sec) [ -17400.0498] [ 2899] [depth= 16] . ( 4 sec) [ -16905.5844] [ 2864] [depth= 14] . ( 4 sec) [ -16819.9383] [ 2889] [depth= 1] . ( 4 sec) [ -16692.7789] [ 2894] [depth= 1] . ( 4 sec) [ -16406.2105] [ 2845] [depth= 11] . ( 4 sec) [ -16265.3904] [ 2833] [depth= 1] . ( 4 sec) [ -16187.9049] [ 2820] [depth= 11] . ( 4 sec) [ -15851.5910] [ 2820] [depth= 11] . ( 4 sec) [ -15821.5513] [ 2817] [depth= 1] . ( 4 sec) [ -15772.5314] [ 2771] [depth= 10] . ( 5 sec) [ -15633.5741] [ 2758] [depth= 8] . ( 5 sec) [ -15582.7323] [ 2743] [depth= 13] . ( 5 sec) [ -15366.1610] [ 2738] [depth= 1] . ( 5 sec) [ -15265.5811] [ 2736] [depth= 10] . ( 5 sec) [ -15218.1155] [ 2735] [depth= 14] . ( 5 sec) [ -15135.2570] [ 2727] [depth= 1] . ( 5 sec) [ -15058.5474] [ 2693] [depth= 7] . ( 5 sec) [ -14977.2072] [ 2670] [depth= 1] . ( 5 sec) [ -14862.7351] [ 2637] [depth= 8] . ( 5 sec) [ -14845.2774] [ 2627] [depth= 1] . ( 5 sec) [ -14807.7374] [ 2624] [depth= 1] . ( 5 sec) [ -14782.1035] [ 2615] [depth= 12] . ( 6 sec) [ -14718.6157] [ 2599] [depth= 11] . ( 6 sec) [ -14715.1206] [ 2597] [depth= 1] . ( 6 sec) [ -14688.1363] [ 2598] [depth= 3] . ( 6 sec) [ -14612.4610] [ 2567] [depth= 3] . ( 6 sec) [ -14295.2767] [ 2558] [depth= 3] . ( 6 sec) [ -14279.4859] [ 2555] [depth= 2] . ( 6 sec) [ -14231.5274] [ 2549] [depth= 3] . ( 6 sec) [ -14209.6972] [ 2546] [depth= 3] . ( 6 sec) [ -14053.3627] [ 2527] [depth= 10] . ( 6 sec) [ -13979.9559] [ 2520] [depth= 8] . ( 6 sec) [ -13974.6655] [ 2522] [depth= 1] . ( 6 sec) [ -13940.3406] [ 2518] [depth= 1] . ( 7 sec) [ -13915.8458] [ 2521] [depth= 1] . ( 7 sec) [ -13803.1192] [ 2506] [depth= 12] . ( 7 sec) [ -13769.1302] [ 2500] [depth= 2] . ( 7 sec) [ -13508.6454] [ 2495] [depth= 8] . ( 7 sec) [ -13360.9356] [ 2428] [depth= 6] . ( 7 sec) [ -13338.3337] [ 2402] [depth= 8] . ( 7 sec) [ -13337.9442] [ 2401] [depth= 1] . ( 7 sec) [ -13311.5154] [ 2392] [depth= 4] . ( 7 sec) [ -13165.0269] [ 2353] [depth= 14] . ( 7 sec) [ -13150.7931] [ 2351] [depth= 1] . ( 7 sec) [ -13147.8252] [ 2346] [depth= 5] . ( 7 sec) [ -13138.3147] [ 2343] [depth= 6] . ( 8 sec) [ -13133.1751] [ 2339] [depth= 2] . ( 8 sec) [ -13123.1559] [ 2333] [depth= 3] . ( 8 sec) [ -13107.6120] [ 2329] [depth= 1] . ( 8 sec) [ -13063.7656] [ 2330] [depth= 8] . ( 8 sec) [ -12773.3285] [ 2252] [depth= 11] . ( 8 sec) [ -12703.9862] [ 2232] [depth= 4] . ( 8 sec) [ -12672.8182] [ 2226] [depth= 4] . ( 8 sec) [ -12652.4243] [ 2222] [depth= 1] . ( 8 sec) [ -12635.8885] [ 2226] [depth= 1] . ( 8 sec) [ -12633.4111] [ 2226] [depth= 2] . ( 8 sec) [ -12623.3862] [ 2222] [depth= 1] . ( 8 sec) [ -12612.7262] [ 2221] [depth= 2] . ( 9 sec) [ -12594.0090] [ 2218] [depth= 8] . ( 9 sec) [ -12532.8379] [ 2217] [depth= 1] . ( 9 sec) [ -12531.9013] [ 2214] [depth= 4] . ( 9 sec) [ -12463.2855] [ 2199] [depth= 1] . ( 9 sec) [ -12454.6026] [ 2182] [depth= 5] . ( 9 sec) [ -12418.8921] [ 2183] [depth= 4] . ( 9 sec) [ -12357.0735] [ 2183] [depth= 3] . ( 9 sec) [ -12351.7073] [ 2181] [depth= 1] . ( 9 sec) [ -12344.8701] [ 2177] [depth= 2] . ( 9 sec) [ -12342.9000] [ 2182] [depth= 1] . ( 10 sec) [ -12329.8333] [ 2177] [depth= 1] . ( 10 sec) [ -12302.6866] [ 2174] [depth= 5] . ( 10 sec) [ -12287.9970] [ 2169] [depth= 2] . ( 10 sec) [ -12247.2104] [ 2170] [depth= 5] . ( 10 sec) [ -12245.0383] [ 2172] [depth= 1] . ( 10 sec) [ -12235.9137] [ 2165] [depth= 6] . ( 10 sec) [ -12211.1051] [ 2163] [depth= 1] . ( 10 sec) [ -12208.7781] [ 2164] [depth= 8] . ( 10 sec) [ -12197.1250] [ 2167] [depth= 8] . ( 10 sec) [ -12185.9556] [ 2161] [depth= 1] . ( 11 sec) [ -12134.1156] [ 2151] [depth= 7] . ( 11 sec) [ -12118.3234] [ 2149] [depth= 2] . ( 11 sec) [ -12113.5881] [ 2148] [depth= 1] . ( 11 sec) [ -12076.2108] [ 2152] [depth= 5] . ( 11 sec) [ -12027.5024] [ 2145] [depth= 1] . ( 11 sec) [ -12026.0834] [ 2145] [depth= 1] . ( 11 sec) [ -12021.1376] [ 2143] [depth= 1] . ( 11 sec) [ -12012.6453] [ 2141] [depth= 1] . ( 11 sec) [ -11951.9549] [ 2129] [depth= 1] . ( 11 sec) [ -11950.5443] [ 2128] [depth= 1] . ( 11 sec) [ -11949.9204] [ 2128] [depth= 1] . ( 12 sec) [ -11941.6053] [ 2126] [depth= 3] . ( 12 sec) [ -11859.0748] [ 2123] [depth= 1] . ( 12 sec) [ -11852.3519] [ 2117] [depth= 4] . ( 12 sec) [ -11821.8110] [ 2123] [depth= 1] . ( 12 sec) [ -11813.5357] [ 2122] [depth= 4] . ( 12 sec) [ -11812.9529] [ 2121] [depth= 1] . ( 12 sec) [ -11811.1616] [ 2121] [depth= 1] . ( 12 sec) [ -11704.0608] [ 2059] [depth= 5] . ( 12 sec) [ -11679.2534] [ 2051] [depth= 5] . ( 13 sec) [ -11679.0984] [ 2050] [depth= 1] . ( 13 sec) [ -11667.0533] [ 2050] [depth= 1] . ( 13 sec) [ -11666.8580] [ 2039] [depth= 8] . ( 13 sec) [ -11565.3260] [Branch lengths ] . ( 17 sec) [ -11395.2366] [GTR parameters ] . ( 18 sec) [ -11269.8707] [Alpha ][ 0.250961] . ( 18 sec) [ -11259.2020] [ 2034] [depth= 1] . ( 18 sec) [ -11257.7675] [ 2033] [depth= 1] . ( 18 sec) [ -11255.1958] [ 2033] [depth= 1] . ( 18 sec) [ -11255.1683] [ 2033] [depth= 2] . ( 18 sec) [ -11234.4377] [ 2024] [depth= 4] . ( 18 sec) [ -11233.3745] [ 2024] [depth= 1] . ( 19 sec) [ -11229.8914] [ 2017] [depth= 4] . ( 19 sec) [ -11212.4272] [ 2024] [depth= 3] . ( 19 sec) [ -11210.3450] [ 2024] [depth= 1] . ( 19 sec) [ -11209.9758] [ 2025] [depth= 1] . ( 19 sec) [ -11208.1555] [ 2025] [depth= 3] . ( 19 sec) [ -11208.0599] [ 2025] [depth= 2] . ( 20 sec) [ -11162.0436] [ 2002] [depth= 4] . ( 20 sec) [ -11155.7514] [ 2010] [depth= 1] . ( 20 sec) [ -11155.5622] [ 2010] [depth= 2] . ( 20 sec) [ -11145.3461] [ 2003] [depth= 1] . ( 21 sec) [ -11141.3664] [ 2003] [depth= 1] . ( 21 sec) [ -11139.0896] [ 2001] [depth= 1] . ( 21 sec) [ -11137.1378] [ 2000] [depth= 2] . ( 21 sec) [ -11080.0115] [ 1966] [depth= 1] . ( 21 sec) [ -11067.9554] [ 1963] [depth= 1] . ( 21 sec) [ -11065.8724] [ 1960] [depth= 1] . ( 22 sec) [ -11065.8218] [ 1961] [depth= 1] . ( 22 sec) [ -11058.5935] [ 1959] [depth= 1] . ( 22 sec) [ -11057.4998] [ 1958] [depth= 1] . ( 22 sec) [ -11055.6230] [ 1957] [depth= 1] . ( 22 sec) [ -11046.3058] [ 1953] [depth= 3] . ( 22 sec) [ -11040.5149] [ 1950] [depth= 1] . ( 23 sec) [ -11040.1812] [ 1950] [depth= 1] . ( 23 sec) [ -11039.6805] [ 1949] [depth= 2] . ( 23 sec) [ -11039.2309] [ 1949] [depth= 1] . ( 23 sec) [ -11035.5356] [ 1948] [depth= 2] . ( 23 sec) [ -11034.8569] [ 1949] [depth= 1] . ( 24 sec) [ -11008.2208] [ 1958] [depth= 1] . ( 24 sec) [ -11007.7600] [ 1957] [depth= 1] . ( 24 sec) [ -11005.4541] [ 1957] [depth= 1] . ( 24 sec) [ -11004.8199] [ 1958] [depth= 1] . ( 24 sec) [ -10999.7729] [ 1955] [depth= 1] . ( 24 sec) [ -10998.3150] [ 1955] [depth= 1] . ( 24 sec) [ -10996.7733] [ 1953] [depth= 1] . ( 25 sec) [ -10996.7490] [ 1953] [depth= 2] . ( 25 sec) [ -10995.5254] [ 1953] [depth= 1] . ( 25 sec) [ -10995.2378] [ 1950] [depth= 1] . ( 26 sec) [ -10992.5749] [ 1943] [depth= 2] . ( 26 sec) [ -10988.0716] [ 1943] [depth= 1] . ( 26 sec) [ -10985.1966] [ 1943] [depth= 1] . ( 27 sec) [ -10983.6646] [ 1944] [depth= 1] . ( 28 sec) [ -10982.5596] [ 1943] [depth= 2] . ( 30 sec) [ -10982.5406] [ 1943] [depth= 2] . ( 30 sec) [ -10960.0121] [Branch lengths ] . ( 34 sec) [ -10955.3192] [GTR parameters ] . ( 34 sec) [ -10951.6736] [Alpha ][ 0.219425] . ( 34 sec) [ -10951.6315] [ 1943] [depth= 2] . ( 40 sec) [ -10951.3594] [ 1945] [depth= 3] . ( 52 sec) [ -10949.5216] [Branch lengths ] . ( 53 sec) [ -10949.5211] [GTR parameters ] . ( 53 sec) [ -10949.4692] [Alpha ][ 0.216044] . ( 72 sec) [ -10949.3229] [Branch lengths ] . ( 130 sec) [ -10949.3062] [Branch lengths ] . ( 130 sec) [ -10949.3062] [Topology ] . ( 131 sec) [ -10949.2704] [Topology ] . ( 133 sec) [ -10949.0143] [Topology ] . ( 134 sec) [ -10947.5847] [Topology ] . ( 135 sec) [ -10943.5058] [Topology ] . ( 137 sec) [ -10940.0505] [Topology ] . ( 138 sec) [ -10939.0604] [Topology ] . ( 141 sec) [ -10939.0027] [GTR parameters ] . ( 141 sec) [ -10938.9963] [Alpha ][ 0.214782] . ( 141 sec) [ -10938.9963] [Topology ] . ( 143 sec) [ -10938.8373] [Topology ] . ( 144 sec) [ -10938.8013] [Topology ] . ( 146 sec) [ -10938.7906] [Topology ] . ( 147 sec) [ -10938.7868] [Topology ] . ( 148 sec) [ -10938.7853] [Topology ] . ( 150 sec) [ -10938.7847] [Topology ] . ( 150 sec) [ -10938.7843] [GTR parameters ] . ( 151 sec) [ -10938.7843] [Alpha ][ 0.214782] . ( 151 sec) [ -10938.7843] [Topology ] . ( 152 sec) [ -10938.7840] [Topology ] . ( 153 sec) [ -10938.7840] [GTR parameters ] . ( 153 sec) [ -10938.7840] [Alpha ][ 0.214782] . Checking for NNIs, optimizing five branches... . ( 164 sec) [ -10938.6930] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10938.693048. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -11527.8412] [GTR parameters ] . ( 3 sec) [ -11290.9171] [Alpha ][ 0.500960] . ( 3 sec) [ -11290.9171] [Topology ] . ( 4 sec) [ -11117.8710] [Topology ] . ( 5 sec) [ -11094.1516] [Topology ] . ( 7 sec) [ -11082.0348] [Topology ] . ( 8 sec) [ -11077.9788] [Topology ] . ( 10 sec) [ -11076.4776] [Topology ] . ( 11 sec) [ -11076.4553] [Topology ] . ( 12 sec) [ -11075.8479] [Topology ] . ( 14 sec) [ -11076.2332] [Topology ] . Moving backward . ( 14 sec) [ -11075.1093] [Topology ] . ( 16 sec) [ -11068.4643] [GTR parameters ] . ( 16 sec) [ -10959.7071] [Alpha ][ 0.250961] . ( 16 sec) [ -10959.7071] [Topology ] . ( 18 sec) [ -10957.4372] [Topology ] . ( 19 sec) [ -10954.7582] [Topology ] . ( 21 sec) [ -10953.6852] [Topology ] . ( 22 sec) [ -10953.4971] [Topology ] . ( 24 sec) [ -10953.4414] [Topology ] . ( 25 sec) [ -10953.4210] [Topology ] . ( 26 sec) [ -10953.4130] [Topology ] . ( 28 sec) [ -10953.4098] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -10951.3573] [GTR parameters ] . ( 40 sec) [ -10948.0561] [Alpha ][ 0.220954] . ( 40 sec) [ -10948.0561] [Topology ] . ( 41 sec) [ -10947.8648] [Topology ] . ( 42 sec) [ -10947.8045] [Topology ] . ( 44 sec) [ -10947.7823] [Topology ] . ( 45 sec) [ -10947.7737] [Topology ] . ( 47 sec) [ -10947.7704] [Topology ] . ( 48 sec) [ -10947.7691] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -10947.6913] [GTR parameters ] . ( 60 sec) [ -10947.6238] [Alpha ][ 0.217056] . ( 60 sec) [ -10947.6238] [Topology ] . ( 61 sec) [ -10947.6183] [Topology ] . ( 63 sec) [ -10947.6165] [Topology ] . ( 64 sec) [ -10947.6159] [Topology ] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -10947.6141] [GTR parameters ] . ( 76 sec) [ -10947.6123] [Alpha ][ 0.216373] . ( 76 sec) [ -10947.6123] [Topology ] . ( 77 sec) [ -10947.6117] [Topology ] . Checking for NNIs, optimizing five branches... . ( 88 sec) [ -10947.6116] [GTR parameters ] . ( 88 sec) [ -10947.6116] [Alpha ][ 0.216373] . ( 88 sec) [ -10947.6116] [Topology ] . ( 90 sec) [ -10947.6114] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 113 sec) [ -11527.8412] [GTR parameters ] . ( 114 sec) [ -11290.9171] [Alpha ][ 0.500960] . ( 114 sec) [ -11290.4691] [ 1959] [depth= 1] . ( 114 sec) [ -11290.1769] [ 1959] [depth= 1] . ( 114 sec) [ -11290.1047] [ 1959] [depth= 1] . ( 115 sec) [ -11289.2190] [ 1959] [depth= 1] . ( 115 sec) [ -11270.6339] [ 1959] [depth= 1] . ( 115 sec) [ -11268.5424] [ 1960] [depth= 1] . ( 115 sec) [ -11255.4173] [ 1959] [depth= 1] . ( 115 sec) [ -11242.4770] [ 1954] [depth= 1] . ( 116 sec) [ -11238.3344] [ 1955] [depth= 3] . ( 116 sec) [ -11219.1425] [ 1953] [depth= 1] . ( 116 sec) [ -11208.3575] [ 1949] [depth= 1] . ( 116 sec) [ -11206.4026] [ 1953] [depth= 1] . ( 116 sec) [ -11204.6450] [ 1952] [depth= 1] . ( 117 sec) [ -11202.1311] [ 1952] [depth= 1] . ( 117 sec) [ -11199.3473] [ 1952] [depth= 1] . ( 117 sec) [ -11196.7907] [ 1953] [depth= 1] . ( 117 sec) [ -11195.3227] [ 1951] [depth= 1] . ( 117 sec) [ -11194.2373] [ 1951] [depth= 1] . ( 118 sec) [ -11194.0336] [ 1951] [depth= 1] . ( 118 sec) [ -11193.6108] [ 1951] [depth= 1] . ( 119 sec) [ -11183.1743] [ 1951] [depth= 1] . ( 119 sec) [ -11181.3775] [ 1951] [depth= 5] . ( 120 sec) [ -11173.5900] [ 1948] [depth= 1] . ( 120 sec) [ -11168.5497] [ 1946] [depth= 1] . ( 121 sec) [ -11166.7899] [ 1946] [depth= 1] . ( 121 sec) [ -11165.7946] [ 1945] [depth= 1] . ( 121 sec) [ -11165.2185] [ 1946] [depth= 1] . ( 121 sec) [ -11164.7793] [ 1945] [depth= 1] . ( 121 sec) [ -11154.6777] [ 1943] [depth= 1] . ( 122 sec) [ -11150.9104] [ 1944] [depth= 1] . ( 122 sec) [ -11148.2190] [ 1942] [depth= 1] . ( 122 sec) [ -11144.7992] [ 1943] [depth= 1] . ( 122 sec) [ -11143.3429] [ 1942] [depth= 1] . ( 122 sec) [ -11141.9461] [ 1945] [depth= 2] . ( 123 sec) [ -11132.2577] [ 1942] [depth= 3] . ( 123 sec) [ -11130.7274] [ 1943] [depth= 1] . ( 123 sec) [ -11130.6639] [ 1943] [depth= 1] . ( 124 sec) [ -11129.0690] [ 1942] [depth= 1] . ( 124 sec) [ -11127.8207] [ 1944] [depth= 1] . ( 124 sec) [ -11127.5787] [ 1947] [depth= 2] . ( 125 sec) [ -11126.6961] [ 1945] [depth= 1] . ( 125 sec) [ -11126.4153] [ 1945] [depth= 2] . ( 125 sec) [ -11125.3180] [ 1941] [depth= 1] . ( 125 sec) [ -11122.2360] [ 1941] [depth= 2] . ( 126 sec) [ -11121.1897] [ 1939] [depth= 1] . ( 126 sec) [ -11120.7593] [ 1939] [depth= 1] . ( 127 sec) [ -11070.5794] [Branch lengths ] . ( 128 sec) [ -11064.6553] [GTR parameters ] . ( 128 sec) [ -10953.2523] [Alpha ][ 0.250961] . ( 135 sec) [ -10952.1908] [ 1940] [depth= 1] . ( 137 sec) [ -10951.4860] [ 1939] [depth= 2] . ( 140 sec) [ -10951.2582] [ 1939] [depth= 1] . ( 144 sec) [ -10946.8764] [Branch lengths ] . ( 144 sec) [ -10944.3053] [GTR parameters ] . ( 145 sec) [ -10941.0273] [Alpha ][ 0.221104] . ( 161 sec) [ -10940.4546] [Branch lengths ] . ( 219 sec) [ -10940.4113] [Branch lengths ] . ( 219 sec) [ -10940.4113] [Topology ] . ( 221 sec) [ -10940.4090] [Topology ] . ( 222 sec) [ -10940.4085] [Topology ] . ( 223 sec) [ -10940.3372] [GTR parameters ] . ( 223 sec) [ -10940.2696] [Alpha ][ 0.217206] . ( 223 sec) [ -10940.2696] [Topology ] . ( 224 sec) [ -10940.2654] [Topology ] . ( 226 sec) [ -10940.2639] [Topology ] . ( 227 sec) [ -10940.2634] [Topology ] . ( 228 sec) [ -10940.2616] [GTR parameters ] . ( 228 sec) [ -10940.2600] [Alpha ][ 0.216571] . ( 228 sec) [ -10940.2600] [Topology ] . ( 229 sec) [ -10940.2595] [Topology ] . ( 230 sec) [ -10940.2594] [GTR parameters ] . ( 230 sec) [ -10940.2594] [Alpha ][ 0.216571] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10947.611398 . Log likelihood obtained after SPR moves : -10940.259448 . Log likelihood of the current tree: -10940.259448. . Printing the most likely tree in file 'nucleic_M2733_60x1207_2006.phy_phyml_tree.txt'... . Best log likelihood : -10938.693048 . Time used 0h4m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1118.24user 0.00system 18:45.68elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps