.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -43176.9977] [GTR parameters ] . ( 5 sec) [ -42211.4051] [Alpha ][ 0.500960] . ( 5 sec) [ -41363.7689] [ 6019] [depth= 13] . ( 5 sec) [ -41235.4705] [ 5957] [depth= 12] . ( 6 sec) [ -40835.1744] [ 5842] [depth= 10] . ( 6 sec) [ -40756.8534] [ 5781] [depth= 1] . ( 6 sec) [ -40466.1235] [ 5684] [depth= 9] . ( 6 sec) [ -40373.1195] [ 5674] [depth= 1] . ( 6 sec) [ -40361.8749] [ 5670] [depth= 7] . ( 6 sec) [ -40266.4376] [ 5650] [depth= 3] . ( 6 sec) [ -40011.4537] [ 5642] [depth= 8] . ( 6 sec) [ -39156.2317] [ 5624] [depth= 5] . ( 6 sec) [ -36926.4946] [ 5620] [depth= 6] . ( 7 sec) [ -36636.6455] [ 5607] [depth= 2] . ( 7 sec) [ -34975.1851] [ 5598] [depth= 7] . ( 7 sec) [ -34797.0678] [ 5513] [depth= 8] . ( 7 sec) [ -34712.4996] [ 5510] [depth= 10] . ( 7 sec) [ -34048.3330] [ 5455] [depth= 5] . ( 7 sec) [ -33563.0299] [ 5466] [depth= 2] . ( 7 sec) [ -33251.5061] [ 5436] [depth= 2] . ( 7 sec) [ -33171.2220] [ 5415] [depth= 22] . ( 8 sec) [ -31451.2105] [ 5372] [depth= 6] . ( 8 sec) [ -31168.8286] [ 5372] [depth= 4] . ( 8 sec) [ -30812.5313] [ 5317] [depth= 15] . ( 8 sec) [ -30256.8143] [ 5317] [depth= 3] . ( 8 sec) [ -30125.9629] [ 5316] [depth= 1] . ( 8 sec) [ -29789.8876] [ 5295] [depth= 15] . ( 8 sec) [ -29789.5033] [ 5295] [depth= 3] . ( 8 sec) [ -29777.3289] [ 5293] [depth= 14] . ( 9 sec) [ -28093.0905] [ 5246] [depth= 1] . ( 9 sec) [ -27796.9200] [ 5194] [depth= 14] . ( 9 sec) [ -27179.0811] [ 5163] [depth= 3] . ( 9 sec) [ -27160.9501] [ 5135] [depth= 1] . ( 9 sec) [ -26926.7791] [ 5110] [depth= 12] . ( 9 sec) [ -26828.0692] [ 5083] [depth= 2] . ( 9 sec) [ -26827.9486] [ 5063] [depth= 1] . ( 9 sec) [ -26808.7701] [ 4984] [depth= 5] . ( 10 sec) [ -26218.2403] [ 4953] [depth= 1] . ( 10 sec) [ -25575.6399] [ 4880] [depth= 2] . ( 10 sec) [ -25327.7047] [ 4817] [depth= 11] . ( 10 sec) [ -25274.2582] [ 4789] [depth= 2] . ( 10 sec) [ -25166.2063] [ 4744] [depth= 15] . ( 10 sec) [ -25121.2837] [ 4742] [depth= 7] . ( 10 sec) [ -25099.3793] [ 4739] [depth= 10] . ( 10 sec) [ -25088.1943] [ 4780] [depth= 1] . ( 11 sec) [ -24308.3883] [ 4644] [depth= 4] . ( 11 sec) [ -24257.0452] [ 4644] [depth= 1] . ( 11 sec) [ -24245.2694] [ 4587] [depth= 9] . ( 11 sec) [ -24230.4225] [ 4587] [depth= 2] . ( 11 sec) [ -24177.7241] [ 4587] [depth= 5] . ( 11 sec) [ -23622.4569] [ 4488] [depth= 6] . ( 11 sec) [ -23583.0598] [ 4485] [depth= 8] . ( 11 sec) [ -23473.7030] [ 4477] [depth= 3] . ( 12 sec) [ -22963.2645] [ 4434] [depth= 2] . ( 12 sec) [ -22869.0984] [ 4408] [depth= 17] . ( 12 sec) [ -22861.9644] [ 4395] [depth= 8] . ( 12 sec) [ -22685.8831] [ 4390] [depth= 2] . ( 12 sec) [ -22287.5646] [ 4333] [depth= 7] . ( 12 sec) [ -22285.0748] [ 4333] [depth= 10] . ( 12 sec) [ -22115.4423] [ 4293] [depth= 5] . ( 13 sec) [ -21423.6937] [ 4259] [depth= 4] . ( 13 sec) [ -20981.0538] [ 4250] [depth= 5] . ( 13 sec) [ -20946.6718] [ 4240] [depth= 7] . ( 13 sec) [ -20896.0422] [ 4239] [depth= 1] . ( 13 sec) [ -20877.9786] [ 4211] [depth= 11] . ( 13 sec) [ -20785.3728] [ 4211] [depth= 8] . ( 13 sec) [ -20782.9604] [ 4211] [depth= 1] . ( 13 sec) [ -20775.6132] [ 4212] [depth= 7] . ( 14 sec) [ -20764.7163] [ 4185] [depth= 8] . ( 14 sec) [ -20071.5286] [ 4185] [depth= 3] . ( 14 sec) [ -19958.3312] [ 4072] [depth= 7] . ( 14 sec) [ -19954.9573] [ 4076] [depth= 1] . ( 14 sec) [ -19774.5674] [ 4044] [depth= 4] . ( 14 sec) [ -19768.3142] [ 4064] [depth= 5] . ( 14 sec) [ -19425.3871] [ 3974] [depth= 2] . ( 15 sec) [ -19273.2915] [ 3957] [depth= 18] . ( 15 sec) [ -18878.1053] [ 3891] [depth= 14] . ( 15 sec) [ -18818.6276] [ 3843] [depth= 14] . ( 15 sec) [ -18818.4213] [ 3843] [depth= 1] . ( 15 sec) [ -18770.2087] [ 3822] [depth= 5] . ( 15 sec) [ -18296.1317] [ 3756] [depth= 2] . ( 15 sec) [ -18282.9149] [ 3741] [depth= 19] . ( 16 sec) [ -18228.8505] [ 3744] [depth= 1] . ( 16 sec) [ -18228.1404] [ 3744] [depth= 1] . ( 16 sec) [ -17659.2173] [ 3706] [depth= 8] . ( 16 sec) [ -17043.9694] [ 3628] [depth= 6] . ( 16 sec) [ -16989.3723] [ 3627] [depth= 1] . ( 16 sec) [ -16970.3361] [ 3607] [depth= 4] . ( 16 sec) [ -16884.8239] [ 3569] [depth= 5] . ( 17 sec) [ -16778.1404] [ 3467] [depth= 11] . ( 17 sec) [ -16202.9819] [ 3438] [depth= 1] . ( 17 sec) [ -16177.5783] [ 3425] [depth= 4] . ( 17 sec) [ -16163.0166] [ 3425] [depth= 7] . ( 17 sec) [ -16085.8252] [ 3417] [depth= 3] . ( 17 sec) [ -16075.2610] [ 3417] [depth= 1] . ( 17 sec) [ -16056.9614] [ 3417] [depth= 1] . ( 18 sec) [ -15749.8536] [ 3314] [depth= 4] . ( 18 sec) [ -15729.7742] [ 3315] [depth= 1] . ( 18 sec) [ -15721.9002] [ 3315] [depth= 3] . ( 18 sec) [ -15715.6342] [ 3315] [depth= 1] . ( 18 sec) [ -15703.8822] [ 3303] [depth= 2] . ( 18 sec) [ -15702.8823] [ 3303] [depth= 3] . ( 18 sec) [ -15701.1704] [ 3303] [depth= 6] . ( 19 sec) [ -15693.3007] [ 3303] [depth= 4] . ( 19 sec) [ -15683.0539] [ 3303] [depth= 2] . ( 19 sec) [ -15636.2239] [ 3285] [depth= 1] . ( 19 sec) [ -15502.9166] [ 3267] [depth= 4] . ( 19 sec) [ -15037.9500] [ 3205] [depth= 9] . ( 19 sec) [ -14476.5215] [ 3180] [depth= 1] . ( 19 sec) [ -14436.5931] [ 3177] [depth= 8] . ( 19 sec) [ -14346.4486] [ 3177] [depth= 1] . ( 20 sec) [ -14248.0687] [ 3166] [depth= 10] . ( 20 sec) [ -14217.2866] [ 3166] [depth= 13] . ( 20 sec) [ -14217.0975] [ 3166] [depth= 4] . ( 20 sec) [ -14202.0161] [ 3165] [depth= 5] . ( 20 sec) [ -14176.9988] [ 3155] [depth= 13] . ( 20 sec) [ -14176.9281] [ 3154] [depth= 6] . ( 20 sec) [ -14176.3728] [ 3154] [depth= 1] . ( 21 sec) [ -14171.0848] [ 3156] [depth= 1] . ( 21 sec) [ -14148.4488] [ 3111] [depth= 2] . ( 21 sec) [ -14044.0967] [ 3107] [depth= 5] . ( 21 sec) [ -13973.7171] [ 3090] [depth= 11] . ( 21 sec) [ -13960.3046] [ 3089] [depth= 1] . ( 21 sec) [ -13861.5575] [ 3060] [depth= 1] . ( 21 sec) [ -13853.1114] [ 3060] [depth= 1] . ( 21 sec) [ -13724.5607] [ 3014] [depth= 16] . ( 22 sec) [ -13723.7848] [ 3014] [depth= 4] . ( 22 sec) [ -13692.6944] [ 3014] [depth= 1] . ( 22 sec) [ -13669.4453] [ 3006] [depth= 3] . ( 22 sec) [ -13661.3619] [ 3006] [depth= 1] . ( 22 sec) [ -13499.0538] [ 2988] [depth= 12] . ( 22 sec) [ -13425.7803] [ 2987] [depth= 3] . ( 22 sec) [ -13407.2553] [ 2979] [depth= 3] . ( 23 sec) [ -13305.2188] [ 2907] [depth= 11] . ( 23 sec) [ -13298.0346] [ 2913] [depth= 1] . ( 23 sec) [ -13230.2075] [ 2885] [depth= 2] . ( 23 sec) [ -13171.0792] [ 2841] [depth= 8] . ( 23 sec) [ -13170.9133] [ 2841] [depth= 1] . ( 23 sec) [ -13094.4979] [ 2824] [depth= 2] . ( 23 sec) [ -13059.6446] [ 2828] [depth= 4] . ( 24 sec) [ -13046.4042] [ 2827] [depth= 6] . ( 24 sec) [ -13013.1080] [ 2805] [depth= 5] . ( 24 sec) [ -13013.0603] [ 2805] [depth= 5] . ( 24 sec) [ -13013.0202] [ 2805] [depth= 2] . ( 25 sec) [ -13013.0076] [ 2805] [depth= 2] . ( 25 sec) [ -13012.9759] [ 2805] [depth= 2] . ( 25 sec) [ -13012.6354] [ 2805] [depth= 1] . ( 25 sec) [ -13011.8041] [ 2802] [depth= 1] . ( 25 sec) [ -12995.8271] [ 2799] [depth= 1] . ( 25 sec) [ -12942.7547] [ 2799] [depth= 1] . ( 26 sec) [ -12874.2962] [ 2782] [depth= 2] . ( 26 sec) [ -12861.7253] [ 2759] [depth= 4] . ( 26 sec) [ -12858.1183] [ 2760] [depth= 3] . ( 26 sec) [ -12858.0860] [ 2764] [depth= 1] . ( 26 sec) [ -12857.4085] [ 2764] [depth= 1] . ( 26 sec) [ -12656.1362] [ 2732] [depth= 3] . ( 26 sec) [ -12654.5178] [ 2734] [depth= 4] . ( 27 sec) [ -12654.2950] [ 2734] [depth= 1] . ( 27 sec) [ -12653.4154] [ 2734] [depth= 1] . ( 27 sec) [ -12641.8944] [ 2735] [depth= 2] . ( 28 sec) [ -12339.3453] [Branch lengths ] . ( 32 sec) [ -12204.5711] [GTR parameters ] . ( 32 sec) [ -12160.9715] [Alpha ][ 0.322383] . ( 32 sec) [ -12155.0136] [ 2729] [depth= 1] . ( 32 sec) [ -12154.9876] [ 2729] [depth= 1] . ( 33 sec) [ -12130.4559] [ 2713] [depth= 5] . ( 33 sec) [ -12130.1669] [ 2713] [depth= 2] . ( 34 sec) [ -12130.1559] [ 2713] [depth= 1] . ( 34 sec) [ -12130.1390] [ 2713] [depth= 1] . ( 34 sec) [ -12128.0411] [ 2718] [depth= 2] . ( 35 sec) [ -12127.7930] [ 2718] [depth= 5] . ( 35 sec) [ -12127.7734] [ 2718] [depth= 6] . ( 35 sec) [ -12117.6676] [ 2718] [depth= 1] . ( 36 sec) [ -12117.3082] [ 2718] [depth= 1] . ( 36 sec) [ -12116.8690] [ 2718] [depth= 1] . ( 37 sec) [ -12116.8588] [ 2718] [depth= 5] . ( 37 sec) [ -12116.8455] [ 2718] [depth= 1] . ( 37 sec) [ -12115.5359] [ 2715] [depth= 2] . ( 38 sec) [ -12115.1782] [ 2714] [depth= 1] . ( 38 sec) [ -12115.1010] [ 2714] [depth= 2] . ( 39 sec) [ -12108.1695] [ 2710] [depth= 1] . ( 40 sec) [ -12107.9942] [ 2710] [depth= 6] . ( 43 sec) [ -12075.6014] [ 2688] [depth= 6] . ( 44 sec) [ -12075.5321] [ 2688] [depth= 1] . ( 45 sec) [ -12075.2228] [ 2688] [depth= 1] . ( 45 sec) [ -12074.3427] [ 2688] [depth= 1] . ( 46 sec) [ -12069.4492] [ 2681] [depth= 1] . ( 46 sec) [ -12068.6916] [ 2686] [depth= 3] . ( 47 sec) [ -12063.3786] [ 2679] [depth= 2] . ( 49 sec) [ -12063.3679] [ 2679] [depth= 4] . ( 50 sec) [ -12060.6895] [ 2678] [depth= 6] . ( 50 sec) [ -12059.6711] [ 2678] [depth= 5] . ( 51 sec) [ -12059.5935] [ 2678] [depth= 2] . ( 51 sec) [ -12059.1231] [ 2677] [depth= 1] . ( 51 sec) [ -12056.8362] [ 2682] [depth= 1] . ( 54 sec) [ -12052.7654] [ 2682] [depth= 1] . ( 55 sec) [ -12052.5716] [ 2682] [depth= 7] . ( 62 sec) [ -12052.1073] [ 2682] [depth= 1] . ( 63 sec) [ -12029.8159] [Branch lengths ] . ( 65 sec) [ -12027.5917] [GTR parameters ] . ( 65 sec) [ -12026.9533] [Alpha ][ 0.306361] . ( 65 sec) [ -12026.7916] [ 2687] [depth= 2] . ( 71 sec) [ -12026.7610] [ 2687] [depth= 1] . ( 80 sec) [ -12026.4675] [ 2691] [depth= 1] . ( 86 sec) [ -12026.4475] [ 2691] [depth= 1] . ( 98 sec) [ -12023.5730] [Branch lengths ] . ( 100 sec) [ -12023.4736] [GTR parameters ] . ( 100 sec) [ -12023.4528] [Alpha ][ 0.303457] . ( 134 sec) [ -12022.9734] [Branch lengths ] . ( 211 sec) [ -12022.8019] [Branch lengths ] . ( 211 sec) [ -12022.8019] [Topology ] . ( 213 sec) [ -12022.7726] [Topology ] . ( 215 sec) [ -12022.7592] [Topology ] . ( 216 sec) [ -12022.7529] [Topology ] . ( 218 sec) [ -12022.7499] [Topology ] . ( 220 sec) [ -12022.7483] [Topology ] . ( 222 sec) [ -12022.7475] [Topology ] . ( 223 sec) [ -12022.7113] [GTR parameters ] . ( 224 sec) [ -12022.7072] [Alpha ][ 0.302166] . ( 224 sec) [ -12022.7072] [Topology ] . ( 225 sec) [ -12022.7005] [Topology ] . ( 227 sec) [ -12022.6984] [Topology ] . ( 229 sec) [ -12022.7008] [Topology ] . Moving backward . ( 229 sec) [ -12022.6967] [Topology ] . ( 231 sec) [ -12022.6973] [Topology ] . ( 232 sec) [ -12022.6950] [GTR parameters ] . ( 232 sec) [ -12022.6948] [Alpha ][ 0.301864] . ( 232 sec) [ -12022.6948] [Topology ] . ( 234 sec) [ -12022.7033] [Topology ] . Moving backward . ( 234 sec) [ -12022.6925] [Topology ] . ( 236 sec) [ -12022.6966] [Topology ] . Moving backward . ( 236 sec) [ -12022.6916] [Topology ] . ( 237 sec) [ -12022.6915] [GTR parameters ] . ( 237 sec) [ -12022.6915] [Alpha ][ 0.301864] . ( 237 sec) [ -12022.6915] [Topology ] . ( 239 sec) [ -12022.6939] [Topology ] . Moving backward . ( 239 sec) [ -12022.6905] [Topology ] . ( 239 sec) [ -12022.6905] [GTR parameters ] . ( 240 sec) [ -12022.6905] [Alpha ][ 0.301864] . ( 240 sec) [ -12022.6905] [Topology ] . ( 241 sec) [ -12022.6918] [Topology ] . Moving backward . ( 242 sec) [ -12022.6900] [Topology ] . ( 242 sec) [ -12022.6900] [GTR parameters ] . ( 242 sec) [ -12022.6900] [Alpha ][ 0.301864] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12022.689953. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -38803.7173] [GTR parameters ] . ( 1 sec) [ -37855.4802] [Alpha ][ 0.500960] . ( 1 sec) [ -37340.1248] [ 5704] [depth= 7] . ( 1 sec) [ -36853.5300] [ 5670] [depth= 7] . ( 1 sec) [ -36702.8155] [ 5646] [depth= 1] . ( 2 sec) [ -36651.6989] [ 5639] [depth= 7] . ( 2 sec) [ -36641.8345] [ 5622] [depth= 1] . ( 2 sec) [ -36385.8354] [ 5611] [depth= 10] . ( 2 sec) [ -35899.6433] [ 5602] [depth= 5] . ( 2 sec) [ -35813.0513] [ 5599] [depth= 8] . ( 2 sec) [ -35729.1052] [ 5569] [depth= 2] . ( 2 sec) [ -35298.9132] [ 5566] [depth= 3] . ( 2 sec) [ -34354.6058] [ 5529] [depth= 12] . ( 2 sec) [ -33096.5968] [ 5526] [depth= 4] . ( 3 sec) [ -32263.8228] [ 5459] [depth= 18] . ( 3 sec) [ -32017.9458] [ 5413] [depth= 8] . ( 3 sec) [ -31812.1034] [ 5423] [depth= 1] . ( 3 sec) [ -31181.4777] [ 5324] [depth= 30] . ( 3 sec) [ -30252.1488] [ 5283] [depth= 28] . ( 3 sec) [ -29985.4252] [ 5191] [depth= 6] . ( 3 sec) [ -29929.9817] [ 5189] [depth= 11] . ( 3 sec) [ -29917.1306] [ 5189] [depth= 10] . ( 4 sec) [ -28502.1408] [ 5123] [depth= 8] . ( 4 sec) [ -27803.1242] [ 5079] [depth= 1] . ( 4 sec) [ -27638.0032] [ 5072] [depth= 22] . ( 4 sec) [ -27173.7379] [ 4976] [depth= 2] . ( 4 sec) [ -27096.6371] [ 4971] [depth= 1] . ( 4 sec) [ -26736.9263] [ 4955] [depth= 4] . ( 4 sec) [ -26521.1685] [ 4888] [depth= 10] . ( 4 sec) [ -26442.4364] [ 4858] [depth= 1] . ( 5 sec) [ -26188.6270] [ 4803] [depth= 8] . ( 5 sec) [ -25693.0725] [ 4734] [depth= 23] . ( 5 sec) [ -25619.1538] [ 4734] [depth= 1] . ( 5 sec) [ -25428.7345] [ 4708] [depth= 6] . ( 5 sec) [ -25287.4947] [ 4700] [depth= 1] . ( 5 sec) [ -25023.4002] [ 4700] [depth= 2] . ( 5 sec) [ -24695.2080] [ 4617] [depth= 20] . ( 5 sec) [ -24609.7020] [ 4617] [depth= 1] . ( 6 sec) [ -24447.1368] [ 4605] [depth= 3] . ( 6 sec) [ -24177.7691] [ 4501] [depth= 8] . ( 6 sec) [ -23866.7818] [ 4470] [depth= 3] . ( 6 sec) [ -23759.5022] [ 4500] [depth= 1] . ( 6 sec) [ -22156.1732] [ 4371] [depth= 18] . ( 6 sec) [ -21736.9744] [ 4286] [depth= 2] . ( 6 sec) [ -21207.0112] [ 4285] [depth= 2] . ( 6 sec) [ -21128.9647] [ 4253] [depth= 1] . ( 7 sec) [ -20932.4363] [ 4166] [depth= 10] . ( 7 sec) [ -20772.0812] [ 4135] [depth= 2] . ( 7 sec) [ -19993.3153] [ 4107] [depth= 16] . ( 7 sec) [ -19861.1250] [ 4017] [depth= 10] . ( 7 sec) [ -19787.6210] [ 4006] [depth= 1] . ( 7 sec) [ -19769.7404] [ 3984] [depth= 16] . ( 7 sec) [ -19763.0119] [ 3985] [depth= 1] . ( 7 sec) [ -19670.8741] [ 3934] [depth= 2] . ( 8 sec) [ -19661.8914] [ 3934] [depth= 11] . ( 8 sec) [ -19625.1417] [ 3946] [depth= 3] . ( 8 sec) [ -19620.2739] [ 3946] [depth= 1] . ( 8 sec) [ -19548.2225] [ 3946] [depth= 1] . ( 8 sec) [ -19547.4136] [ 3946] [depth= 1] . ( 8 sec) [ -19525.7315] [ 3945] [depth= 1] . ( 8 sec) [ -19141.5040] [ 3900] [depth= 6] . ( 9 sec) [ -18918.4904] [ 3888] [depth= 2] . ( 9 sec) [ -18916.3956] [ 3888] [depth= 1] . ( 9 sec) [ -18757.1652] [ 3848] [depth= 7] . ( 9 sec) [ -18731.2353] [ 3848] [depth= 3] . ( 9 sec) [ -18247.5252] [ 3797] [depth= 3] . ( 9 sec) [ -18228.5060] [ 3795] [depth= 2] . ( 9 sec) [ -18200.2201] [ 3792] [depth= 3] . ( 9 sec) [ -17990.5456] [ 3736] [depth= 7] . ( 9 sec) [ -17579.7292] [ 3736] [depth= 2] . ( 9 sec) [ -17561.7670] [ 3717] [depth= 4] . ( 10 sec) [ -17506.2525] [ 3724] [depth= 1] . ( 10 sec) [ -17496.4358] [ 3727] [depth= 4] . ( 10 sec) [ -17382.5753] [ 3726] [depth= 4] . ( 10 sec) [ -17361.6487] [ 3725] [depth= 10] . ( 10 sec) [ -17311.2514] [ 3726] [depth= 5] . ( 10 sec) [ -17234.6064] [ 3715] [depth= 11] . ( 10 sec) [ -17210.3881] [ 3707] [depth= 10] . ( 10 sec) [ -17208.8656] [ 3700] [depth= 1] . ( 11 sec) [ -17208.6828] [ 3700] [depth= 1] . ( 11 sec) [ -17129.8946] [ 3700] [depth= 2] . ( 11 sec) [ -17119.0780] [ 3698] [depth= 6] . ( 11 sec) [ -17067.3404] [ 3698] [depth= 4] . ( 11 sec) [ -17010.8508] [ 3665] [depth= 2] . ( 11 sec) [ -17008.9983] [ 3664] [depth= 4] . ( 11 sec) [ -17008.9649] [ 3664] [depth= 8] . ( 11 sec) [ -17008.6527] [ 3664] [depth= 2] . ( 11 sec) [ -16963.6216] [ 3618] [depth= 6] . ( 12 sec) [ -16960.7278] [ 3618] [depth= 4] . ( 12 sec) [ -16921.7760] [ 3598] [depth= 6] . ( 12 sec) [ -16875.5209] [ 3589] [depth= 5] . ( 12 sec) [ -16836.7104] [ 3555] [depth= 5] . ( 12 sec) [ -16833.7553] [ 3555] [depth= 1] . ( 12 sec) [ -16824.6044] [ 3544] [depth= 2] . ( 12 sec) [ -16824.4342] [ 3544] [depth= 2] . ( 12 sec) [ -16692.4386] [ 3497] [depth= 10] . ( 13 sec) [ -16615.0994] [ 3459] [depth= 5] . ( 13 sec) [ -16583.3722] [ 3459] [depth= 2] . ( 13 sec) [ -16475.8264] [ 3459] [depth= 6] . ( 13 sec) [ -16336.7236] [ 3437] [depth= 9] . ( 13 sec) [ -15453.9173] [ 3402] [depth= 10] . ( 13 sec) [ -15442.6777] [ 3383] [depth= 4] . ( 13 sec) [ -15247.3639] [ 3331] [depth= 1] . ( 13 sec) [ -15065.7927] [ 3223] [depth= 3] . ( 14 sec) [ -14839.0512] [ 3221] [depth= 2] . ( 14 sec) [ -14826.7420] [ 3217] [depth= 4] . ( 14 sec) [ -14800.5649] [ 3214] [depth= 8] . ( 14 sec) [ -14797.7354] [ 3214] [depth= 1] . ( 14 sec) [ -14788.9345] [ 3214] [depth= 16] . ( 14 sec) [ -14783.6794] [ 3214] [depth= 5] . ( 14 sec) [ -14783.0651] [ 3214] [depth= 1] . ( 14 sec) [ -14782.3319] [ 3213] [depth= 8] . ( 15 sec) [ -14779.2880] [ 3216] [depth= 1] . ( 15 sec) [ -14776.6660] [ 3207] [depth= 2] . ( 15 sec) [ -14776.6519] [ 3207] [depth= 8] . ( 15 sec) [ -14756.9236] [ 3207] [depth= 1] . ( 15 sec) [ -14756.8679] [ 3207] [depth= 5] . ( 15 sec) [ -14730.7052] [ 3207] [depth= 2] . ( 15 sec) [ -14592.6294] [ 3174] [depth= 11] . ( 15 sec) [ -14536.9371] [ 3159] [depth= 1] . ( 16 sec) [ -14533.3593] [ 3161] [depth= 2] . ( 16 sec) [ -14533.1318] [ 3161] [depth= 1] . ( 16 sec) [ -14533.0312] [ 3161] [depth= 4] . ( 16 sec) [ -14530.8190] [ 3161] [depth= 1] . ( 16 sec) [ -14449.8952] [ 3075] [depth= 5] . ( 16 sec) [ -14406.1693] [ 3021] [depth= 20] . ( 16 sec) [ -14352.3803] [ 3024] [depth= 2] . ( 17 sec) [ -14341.6363] [ 3024] [depth= 1] . ( 17 sec) [ -14341.1858] [ 3024] [depth= 2] . ( 17 sec) [ -14341.1323] [ 3024] [depth= 4] . ( 17 sec) [ -14251.0657] [ 3013] [depth= 1] . ( 17 sec) [ -14145.8221] [ 2935] [depth= 17] . ( 17 sec) [ -14145.7779] [ 2935] [depth= 1] . ( 17 sec) [ -14145.7080] [ 2935] [depth= 2] . ( 18 sec) [ -14077.1530] [ 2935] [depth= 1] . ( 18 sec) [ -13967.4398] [ 2922] [depth= 2] . ( 18 sec) [ -13954.9184] [ 2928] [depth= 1] . ( 18 sec) [ -13951.3833] [ 2928] [depth= 1] . ( 18 sec) [ -13840.5364] [ 2950] [depth= 1] . ( 18 sec) [ -13775.0613] [ 2950] [depth= 1] . ( 18 sec) [ -13773.5424] [ 2955] [depth= 1] . ( 18 sec) [ -13730.1384] [ 2944] [depth= 2] . ( 19 sec) [ -13577.4397] [ 2872] [depth= 9] . ( 19 sec) [ -13556.9804] [ 2876] [depth= 1] . ( 19 sec) [ -13551.3889] [ 2869] [depth= 1] . ( 19 sec) [ -13549.5876] [ 2869] [depth= 1] . ( 19 sec) [ -13486.8865] [ 2856] [depth= 4] . ( 19 sec) [ -13474.4976] [ 2856] [depth= 1] . ( 19 sec) [ -13473.6767] [ 2856] [depth= 5] . ( 20 sec) [ -13465.3467] [ 2854] [depth= 1] . ( 20 sec) [ -13453.9588] [ 2850] [depth= 6] . ( 21 sec) [ -13377.0875] [ 2846] [depth= 1] . ( 21 sec) [ -13300.2497] [ 2840] [depth= 2] . ( 21 sec) [ -13299.6780] [ 2840] [depth= 6] . ( 21 sec) [ -13272.5895] [ 2843] [depth= 1] . ( 21 sec) [ -13148.1360] [ 2843] [depth= 1] . ( 21 sec) [ -13147.8830] [ 2845] [depth= 1] . ( 21 sec) [ -13133.8402] [ 2845] [depth= 1] . ( 22 sec) [ -13133.3294] [ 2845] [depth= 6] . ( 22 sec) [ -13109.3301] [ 2823] [depth= 4] . ( 22 sec) [ -13109.2544] [ 2823] [depth= 1] . ( 22 sec) [ -13106.5990] [ 2816] [depth= 18] . ( 22 sec) [ -13100.4527] [ 2818] [depth= 1] . ( 22 sec) [ -13053.2598] [ 2814] [depth= 1] . ( 22 sec) [ -13039.5024] [ 2814] [depth= 1] . ( 22 sec) [ -13030.3843] [ 2813] [depth= 2] . ( 22 sec) [ -13026.4643] [ 2806] [depth= 1] . ( 23 sec) [ -13023.0020] [ 2806] [depth= 1] . ( 23 sec) [ -13009.7500] [ 2806] [depth= 1] . ( 23 sec) [ -12956.2472] [ 2802] [depth= 2] . ( 23 sec) [ -12949.5114] [ 2807] [depth= 1] . ( 24 sec) [ -12663.8765] [Branch lengths ] . ( 27 sec) [ -12528.9425] [GTR parameters ] . ( 28 sec) [ -12479.3954] [Alpha ][ 0.312735] . ( 28 sec) [ -12475.4507] [ 2806] [depth= 1] . ( 28 sec) [ -12475.3327] [ 2806] [depth= 6] . ( 28 sec) [ -12404.2829] [ 2761] [depth= 9] . ( 29 sec) [ -12371.3353] [ 2737] [depth= 2] . ( 29 sec) [ -12357.2102] [ 2737] [depth= 1] . ( 29 sec) [ -12354.5991] [ 2737] [depth= 1] . ( 29 sec) [ -12354.5792] [ 2737] [depth= 2] . ( 30 sec) [ -12353.8725] [ 2737] [depth= 3] . ( 30 sec) [ -12353.8453] [ 2737] [depth= 1] . ( 30 sec) [ -12353.1534] [ 2737] [depth= 1] . ( 30 sec) [ -12352.8888] [ 2737] [depth= 1] . ( 31 sec) [ -12351.6105] [ 2737] [depth= 3] . ( 31 sec) [ -12319.5530] [ 2715] [depth= 4] . ( 31 sec) [ -12319.1515] [ 2720] [depth= 1] . ( 32 sec) [ -12319.1363] [ 2720] [depth= 1] . ( 32 sec) [ -12319.1128] [ 2720] [depth= 1] . ( 32 sec) [ -12305.3239] [ 2720] [depth= 1] . ( 32 sec) [ -12305.3048] [ 2720] [depth= 6] . ( 33 sec) [ -12305.1931] [ 2720] [depth= 3] . ( 33 sec) [ -12305.1596] [ 2720] [depth= 1] . ( 34 sec) [ -12304.6803] [ 2720] [depth= 1] . ( 34 sec) [ -12301.5588] [ 2742] [depth= 1] . ( 35 sec) [ -12301.5358] [ 2742] [depth= 4] . ( 35 sec) [ -12301.4474] [ 2742] [depth= 1] . ( 36 sec) [ -12301.4204] [ 2742] [depth= 4] . ( 36 sec) [ -12296.4233] [ 2741] [depth= 3] . ( 37 sec) [ -12296.1123] [ 2741] [depth= 3] . ( 39 sec) [ -12289.2696] [ 2738] [depth= 2] . ( 39 sec) [ -12287.5463] [ 2742] [depth= 1] . ( 41 sec) [ -12287.5288] [ 2742] [depth= 2] . ( 41 sec) [ -12169.1723] [ 2703] [depth= 6] . ( 41 sec) [ -12169.1503] [ 2703] [depth= 2] . ( 42 sec) [ -12169.1388] [ 2703] [depth= 3] . ( 44 sec) [ -12166.7985] [ 2698] [depth= 2] . ( 46 sec) [ -12164.2388] [ 2697] [depth= 1] . ( 46 sec) [ -12163.8985] [ 2709] [depth= 1] . ( 47 sec) [ -12157.9582] [ 2714] [depth= 3] . ( 49 sec) [ -12108.8517] [ 2697] [depth= 1] . ( 49 sec) [ -12104.8128] [ 2697] [depth= 1] . ( 49 sec) [ -12104.8017] [ 2697] [depth= 1] . ( 55 sec) [ -12095.8249] [ 2677] [depth= 4] . ( 55 sec) [ -12093.3825] [ 2681] [depth= 1] . ( 55 sec) [ -12091.5576] [ 2677] [depth= 1] . ( 56 sec) [ -12040.8346] [Branch lengths ] . ( 58 sec) [ -12036.2582] [GTR parameters ] . ( 58 sec) [ -12035.9991] [Alpha ][ 0.302490] . ( 59 sec) [ -12035.4710] [ 2677] [depth= 3] . ( 62 sec) [ -12035.4603] [ 2677] [depth= 1] . ( 63 sec) [ -12034.9381] [ 2682] [depth= 2] . ( 63 sec) [ -12034.9174] [ 2682] [depth= 1] . ( 66 sec) [ -12034.8651] [ 2682] [depth= 1] . ( 66 sec) [ -12034.8375] [ 2682] [depth= 1] . ( 79 sec) [ -12034.6352] [ 2681] [depth= 2] . ( 80 sec) [ -12034.3548] [ 2680] [depth= 1] . ( 90 sec) [ -12028.3333] [Branch lengths ] . ( 91 sec) [ -12028.2119] [GTR parameters ] . ( 92 sec) [ -12028.2071] [Alpha ][ 0.301064] . ( 113 sec) [ -12027.7041] [ 2682] [depth= 1] . ( 122 sec) [ -12027.5033] [ 2683] [depth= 2] . ( 123 sec) [ -12025.6496] [Branch lengths ] . ( 125 sec) [ -12025.5965] [GTR parameters ] . ( 125 sec) [ -12025.5958] [Alpha ][ 0.301533] . ( 156 sec) [ -12025.1889] [Branch lengths ] . ( 233 sec) [ -12024.8867] [Branch lengths ] . ( 233 sec) [ -12024.8867] [Topology ] . ( 235 sec) [ -12024.8642] [Topology ] . ( 237 sec) [ -12024.8571] [Topology ] . ( 239 sec) [ -12024.8541] [Topology ] . ( 241 sec) [ -12024.8527] [Topology ] . ( 242 sec) [ -12024.8520] [Topology ] . ( 244 sec) [ -12024.8199] [GTR parameters ] . ( 244 sec) [ -12024.8178] [Alpha ][ 0.300598] . ( 244 sec) [ -12024.8178] [Topology ] . ( 246 sec) [ -12024.8119] [Topology ] . ( 248 sec) [ -12024.8095] [Topology ] . ( 250 sec) [ -12024.8082] [Topology ] . ( 251 sec) [ -12024.8075] [Topology ] . ( 253 sec) [ -12024.8054] [GTR parameters ] . ( 253 sec) [ -12024.8054] [Alpha ][ 0.300297] . ( 253 sec) [ -12024.8054] [Topology ] . ( 255 sec) [ -12024.8042] [Topology ] . ( 257 sec) [ -12024.8036] [Topology ] . ( 257 sec) [ -12024.8034] [GTR parameters ] . ( 258 sec) [ -12024.8034] [Alpha ][ 0.300297] . ( 258 sec) [ -12024.8034] [Topology ] . ( 259 sec) [ -12024.8029] [Topology ] . ( 260 sec) [ -12024.8028] [GTR parameters ] . ( 260 sec) [ -12024.8028] [Alpha ][ 0.300297] . Checking for NNIs, optimizing five branches... . ( 274 sec) [ -12024.8027] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12024.802736. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -42774.3149] [GTR parameters ] . ( 4 sec) [ -41835.6085] [Alpha ][ 0.500960] . ( 4 sec) [ -41547.1941] [ 5886] [depth= 13] . ( 4 sec) [ -41258.1745] [ 5841] [depth= 12] . ( 4 sec) [ -40933.1254] [ 5799] [depth= 9] . ( 4 sec) [ -40873.2527] [ 5799] [depth= 1] . ( 4 sec) [ -40613.1341] [ 5746] [depth= 12] . ( 4 sec) [ -40518.4445] [ 5744] [depth= 1] . ( 5 sec) [ -40098.9447] [ 5738] [depth= 9] . ( 5 sec) [ -39455.8108] [ 5716] [depth= 3] . ( 5 sec) [ -39398.1355] [ 5716] [depth= 12] . ( 5 sec) [ -39257.3392] [ 5708] [depth= 4] . ( 5 sec) [ -38169.3393] [ 5703] [depth= 6] . ( 5 sec) [ -37592.9607] [ 5662] [depth= 4] . ( 5 sec) [ -36869.2088] [ 5645] [depth= 8] . ( 5 sec) [ -35067.1695] [ 5636] [depth= 6] . ( 5 sec) [ -34576.5018] [ 5634] [depth= 2] . ( 6 sec) [ -33764.2695] [ 5629] [depth= 1] . ( 6 sec) [ -33620.8056] [ 5612] [depth= 8] . ( 6 sec) [ -29974.1387] [ 5598] [depth= 12] . ( 6 sec) [ -29914.0690] [ 5596] [depth= 1] . ( 6 sec) [ -29123.6315] [ 5510] [depth= 10] . ( 6 sec) [ -29101.3163] [ 5508] [depth= 1] . ( 6 sec) [ -29001.3297] [ 5495] [depth= 14] . ( 7 sec) [ -28967.6508] [ 5459] [depth= 9] . ( 7 sec) [ -28881.3058] [ 5442] [depth= 1] . ( 7 sec) [ -28780.6893] [ 5434] [depth= 18] . ( 7 sec) [ -28674.7282] [ 5410] [depth= 2] . ( 7 sec) [ -28423.7342] [ 5393] [depth= 16] . ( 7 sec) [ -27532.7139] [ 5347] [depth= 2] . ( 7 sec) [ -27002.1500] [ 5167] [depth= 21] . ( 8 sec) [ -26946.4814] [ 5167] [depth= 1] . ( 8 sec) [ -26780.4014] [ 5079] [depth= 6] . ( 8 sec) [ -26617.0500] [ 5079] [depth= 12] . ( 8 sec) [ -26112.2538] [ 4999] [depth= 16] . ( 8 sec) [ -25974.8867] [ 5000] [depth= 5] . ( 8 sec) [ -25950.0904] [ 4999] [depth= 1] . ( 8 sec) [ -24250.9574] [ 4986] [depth= 3] . ( 8 sec) [ -24063.1652] [ 4981] [depth= 3] . ( 9 sec) [ -23943.7912] [ 4940] [depth= 7] . ( 9 sec) [ -23804.5405] [ 4928] [depth= 4] . ( 9 sec) [ -23729.8125] [ 4870] [depth= 5] . ( 9 sec) [ -23558.9350] [ 4928] [depth= 1] . ( 9 sec) [ -23408.3597] [ 4854] [depth= 3] . ( 9 sec) [ -23331.7063] [ 4855] [depth= 6] . ( 9 sec) [ -23330.9798] [ 4855] [depth= 14] . ( 9 sec) [ -22753.5550] [ 4724] [depth= 3] . ( 9 sec) [ -22720.2142] [ 4726] [depth= 1] . ( 10 sec) [ -22564.8627] [ 4686] [depth= 1] . ( 10 sec) [ -22414.3744] [ 4664] [depth= 14] . ( 10 sec) [ -21618.5334] [ 4589] [depth= 17] . ( 10 sec) [ -21578.5878] [ 4589] [depth= 14] . ( 10 sec) [ -21546.6052] [ 4564] [depth= 10] . ( 10 sec) [ -21028.3955] [ 4560] [depth= 1] . ( 10 sec) [ -20869.6046] [ 4524] [depth= 9] . ( 11 sec) [ -20819.8889] [ 4524] [depth= 1] . ( 11 sec) [ -20805.8752] [ 4506] [depth= 8] . ( 11 sec) [ -20510.9537] [ 4470] [depth= 1] . ( 11 sec) [ -19865.8941] [ 4351] [depth= 6] . ( 11 sec) [ -19850.2313] [ 4302] [depth= 11] . ( 12 sec) [ -19626.2773] [ 4272] [depth= 4] . ( 12 sec) [ -19416.7774] [ 4240] [depth= 6] . ( 12 sec) [ -19406.2693] [ 4238] [depth= 4] . ( 12 sec) [ -19215.0179] [ 4205] [depth= 6] . ( 12 sec) [ -19187.5698] [ 4189] [depth= 3] . ( 12 sec) [ -18488.7639] [ 4083] [depth= 6] . ( 12 sec) [ -18457.1073] [ 4079] [depth= 1] . ( 12 sec) [ -18327.3487] [ 4044] [depth= 16] . ( 12 sec) [ -18156.1414] [ 4033] [depth= 1] . ( 13 sec) [ -17997.2085] [ 3993] [depth= 4] . ( 13 sec) [ -17942.4364] [ 3993] [depth= 1] . ( 13 sec) [ -17870.9755] [ 3986] [depth= 7] . ( 13 sec) [ -17862.1930] [ 3986] [depth= 1] . ( 13 sec) [ -17862.1323] [ 3986] [depth= 2] . ( 13 sec) [ -17862.0701] [ 3986] [depth= 2] . ( 14 sec) [ -17631.0417] [ 3980] [depth= 4] . ( 14 sec) [ -17573.1125] [ 3910] [depth= 11] . ( 14 sec) [ -17346.0895] [ 3873] [depth= 1] . ( 14 sec) [ -17307.5331] [ 3829] [depth= 5] . ( 14 sec) [ -16898.5353] [ 3707] [depth= 12] . ( 14 sec) [ -16523.5303] [ 3589] [depth= 10] . ( 14 sec) [ -16485.9508] [ 3570] [depth= 2] . ( 15 sec) [ -16405.5859] [ 3561] [depth= 1] . ( 15 sec) [ -16387.3792] [ 3549] [depth= 1] . ( 15 sec) [ -16233.1844] [ 3497] [depth= 7] . ( 15 sec) [ -16192.6811] [ 3441] [depth= 10] . ( 15 sec) [ -16184.4881] [ 3441] [depth= 3] . ( 15 sec) [ -16076.0274] [ 3450] [depth= 4] . ( 15 sec) [ -15869.4747] [ 3414] [depth= 4] . ( 15 sec) [ -15868.5750] [ 3414] [depth= 1] . ( 16 sec) [ -15743.1884] [ 3397] [depth= 12] . ( 16 sec) [ -15573.0557] [ 3363] [depth= 15] . ( 16 sec) [ -15103.9389] [ 3359] [depth= 2] . ( 16 sec) [ -15076.8515] [ 3346] [depth= 6] . ( 16 sec) [ -15058.5118] [ 3330] [depth= 2] . ( 16 sec) [ -15058.3717] [ 3330] [depth= 1] . ( 16 sec) [ -14926.9338] [ 3320] [depth= 8] . ( 17 sec) [ -14926.3666] [ 3320] [depth= 2] . ( 17 sec) [ -14871.9183] [ 3319] [depth= 4] . ( 17 sec) [ -14836.1817] [ 3319] [depth= 15] . ( 17 sec) [ -14773.7924] [ 3309] [depth= 1] . ( 17 sec) [ -14756.4112] [ 3309] [depth= 1] . ( 17 sec) [ -14720.9403] [ 3265] [depth= 3] . ( 17 sec) [ -14649.7176] [ 3233] [depth= 7] . ( 17 sec) [ -14519.1619] [ 3196] [depth= 9] . ( 17 sec) [ -14491.7734] [ 3196] [depth= 1] . ( 18 sec) [ -14490.6357] [ 3196] [depth= 9] . ( 18 sec) [ -14426.6502] [ 3196] [depth= 1] . ( 18 sec) [ -14422.4465] [ 3196] [depth= 4] . ( 18 sec) [ -14421.4623] [ 3196] [depth= 1] . ( 18 sec) [ -14419.8987] [ 3196] [depth= 3] . ( 18 sec) [ -14365.6489] [ 3206] [depth= 1] . ( 18 sec) [ -14354.6986] [ 3196] [depth= 2] . ( 19 sec) [ -14338.6247] [ 3196] [depth= 5] . ( 19 sec) [ -14331.4312] [ 3200] [depth= 7] . ( 19 sec) [ -14298.7325] [ 3202] [depth= 5] . ( 19 sec) [ -14293.3129] [ 3206] [depth= 1] . ( 19 sec) [ -14256.0635] [ 3198] [depth= 3] . ( 19 sec) [ -14201.5779] [ 3194] [depth= 1] . ( 19 sec) [ -14151.2125] [ 3127] [depth= 7] . ( 20 sec) [ -14146.1259] [ 3127] [depth= 1] . ( 20 sec) [ -14098.9875] [ 3113] [depth= 1] . ( 20 sec) [ -14097.6356] [ 3113] [depth= 1] . ( 20 sec) [ -14096.6874] [ 3113] [depth= 5] . ( 20 sec) [ -14082.4091] [ 3113] [depth= 12] . ( 20 sec) [ -14065.6307] [ 3140] [depth= 1] . ( 20 sec) [ -14058.5774] [ 3127] [depth= 6] . ( 21 sec) [ -14050.3452] [ 3124] [depth= 1] . ( 21 sec) [ -14011.1408] [ 3141] [depth= 3] . ( 21 sec) [ -14009.5536] [ 3116] [depth= 7] . ( 21 sec) [ -14006.2087] [ 3116] [depth= 1] . ( 21 sec) [ -14005.9667] [ 3116] [depth= 6] . ( 21 sec) [ -14005.9393] [ 3116] [depth= 8] . ( 21 sec) [ -13994.5347] [ 3083] [depth= 2] . ( 22 sec) [ -13978.5640] [ 3092] [depth= 9] . ( 22 sec) [ -13973.8723] [ 3081] [depth= 7] . ( 22 sec) [ -13964.3588] [ 3081] [depth= 2] . ( 22 sec) [ -13964.2596] [ 3081] [depth= 1] . ( 22 sec) [ -13960.9635] [ 3080] [depth= 5] . ( 23 sec) [ -13891.9792] [ 3059] [depth= 6] . ( 23 sec) [ -13741.6068] [ 3032] [depth= 1] . ( 23 sec) [ -13740.6775] [ 3034] [depth= 3] . ( 23 sec) [ -13707.9144] [ 2995] [depth= 6] . ( 23 sec) [ -13614.8683] [ 2950] [depth= 5] . ( 23 sec) [ -13579.5980] [ 2950] [depth= 1] . ( 24 sec) [ -13578.5530] [ 2950] [depth= 6] . ( 24 sec) [ -13545.3063] [ 2950] [depth= 1] . ( 24 sec) [ -13538.7734] [ 2950] [depth= 1] . ( 24 sec) [ -13538.7257] [ 2950] [depth= 6] . ( 24 sec) [ -13534.8313] [ 2950] [depth= 1] . ( 25 sec) [ -13473.2694] [ 2906] [depth= 5] . ( 25 sec) [ -13372.6827] [ 2900] [depth= 3] . ( 25 sec) [ -13340.8650] [ 2878] [depth= 4] . ( 25 sec) [ -13253.7120] [ 2891] [depth= 2] . ( 25 sec) [ -13252.3941] [ 2891] [depth= 3] . ( 25 sec) [ -13179.0580] [ 2891] [depth= 1] . ( 25 sec) [ -13148.6090] [ 2888] [depth= 2] . ( 26 sec) [ -13146.7613] [ 2888] [depth= 5] . ( 26 sec) [ -13040.7692] [ 2875] [depth= 9] . ( 27 sec) [ -12688.6182] [Branch lengths ] . ( 29 sec) [ -12546.8226] [GTR parameters ] . ( 30 sec) [ -12499.6005] [Alpha ][ 0.321249] . ( 30 sec) [ -12497.1954] [ 2878] [depth= 2] . ( 30 sec) [ -12483.7493] [ 2881] [depth= 1] . ( 31 sec) [ -12470.1896] [ 2875] [depth= 2] . ( 31 sec) [ -12467.6580] [ 2875] [depth= 1] . ( 31 sec) [ -12467.0652] [ 2875] [depth= 3] . ( 31 sec) [ -12462.7201] [ 2865] [depth= 2] . ( 31 sec) [ -12393.0720] [ 2818] [depth= 4] . ( 31 sec) [ -12298.1534] [ 2763] [depth= 5] . ( 31 sec) [ -12297.0709] [ 2763] [depth= 2] . ( 32 sec) [ -12297.0580] [ 2763] [depth= 2] . ( 32 sec) [ -12253.1402] [ 2735] [depth= 4] . ( 32 sec) [ -12253.0452] [ 2735] [depth= 4] . ( 32 sec) [ -12245.4554] [ 2728] [depth= 1] . ( 32 sec) [ -12235.4228] [ 2715] [depth= 1] . ( 33 sec) [ -12235.3156] [ 2717] [depth= 2] . ( 33 sec) [ -12235.2913] [ 2717] [depth= 6] . ( 34 sec) [ -12234.5597] [ 2717] [depth= 3] . ( 34 sec) [ -12227.4478] [ 2715] [depth= 1] . ( 34 sec) [ -12227.3966] [ 2715] [depth= 2] . ( 34 sec) [ -12224.2586] [ 2715] [depth= 1] . ( 35 sec) [ -12223.4366] [ 2715] [depth= 7] . ( 35 sec) [ -12223.4250] [ 2715] [depth= 1] . ( 35 sec) [ -12223.3534] [ 2715] [depth= 1] . ( 36 sec) [ -12223.3150] [ 2715] [depth= 5] . ( 36 sec) [ -12223.2972] [ 2715] [depth= 7] . ( 37 sec) [ -12223.2866] [ 2715] [depth= 4] . ( 37 sec) [ -12220.6957] [ 2717] [depth= 1] . ( 37 sec) [ -12199.5019] [ 2721] [depth= 1] . ( 37 sec) [ -12199.3813] [ 2721] [depth= 8] . ( 37 sec) [ -12197.6356] [ 2723] [depth= 1] . ( 38 sec) [ -12197.3798] [ 2723] [depth= 3] . ( 39 sec) [ -12197.3557] [ 2723] [depth= 1] . ( 39 sec) [ -12197.2916] [ 2723] [depth= 4] . ( 41 sec) [ -12196.5249] [ 2721] [depth= 1] . ( 43 sec) [ -12195.6863] [ 2722] [depth= 2] . ( 43 sec) [ -12192.4695] [ 2721] [depth= 1] . ( 43 sec) [ -12183.7917] [ 2713] [depth= 2] . ( 45 sec) [ -12182.6109] [ 2713] [depth= 1] . ( 45 sec) [ -12161.4140] [ 2700] [depth= 1] . ( 46 sec) [ -12161.3996] [ 2700] [depth= 8] . ( 47 sec) [ -12151.8526] [ 2700] [depth= 1] . ( 47 sec) [ -12151.8387] [ 2700] [depth= 5] . ( 47 sec) [ -12149.7980] [ 2704] [depth= 1] . ( 47 sec) [ -12143.7298] [ 2704] [depth= 1] . ( 49 sec) [ -12113.3553] [ 2687] [depth= 9] . ( 49 sec) [ -12109.9972] [ 2687] [depth= 1] . ( 49 sec) [ -12108.7354] [ 2687] [depth= 1] . ( 50 sec) [ -12103.8762] [ 2686] [depth= 6] . ( 50 sec) [ -12103.8063] [ 2686] [depth= 6] . ( 50 sec) [ -12103.7698] [ 2686] [depth= 5] . ( 53 sec) [ -12103.5744] [ 2686] [depth= 1] . ( 55 sec) [ -12087.6107] [ 2679] [depth= 9] . ( 55 sec) [ -12087.4666] [ 2679] [depth= 2] . ( 55 sec) [ -12087.4546] [ 2679] [depth= 4] . ( 56 sec) [ -12085.9614] [ 2679] [depth= 1] . ( 57 sec) [ -12045.7162] [Branch lengths ] . ( 59 sec) [ -12042.9379] [GTR parameters ] . ( 60 sec) [ -12042.0312] [Alpha ][ 0.301950] . ( 60 sec) [ -12041.3042] [ 2677] [depth= 2] . ( 80 sec) [ -12041.2932] [ 2677] [depth= 3] . ( 81 sec) [ -12040.8223] [ 2676] [depth= 1] . ( 93 sec) [ -12036.6710] [Branch lengths ] . ( 95 sec) [ -12036.5488] [GTR parameters ] . ( 95 sec) [ -12036.5390] [Alpha ][ 0.299940] . ( 127 sec) [ -12035.9549] [Branch lengths ] . ( 127 sec) [ -12035.5050] [ 2682] [depth= 4] . ( 203 sec) [ -12035.1338] [Branch lengths ] . ( 205 sec) [ -12035.1045] [GTR parameters ] . ( 205 sec) [ -12035.1034] [Alpha ][ 0.299238] . ( 205 sec) [ -12035.1034] [Topology ] . ( 207 sec) [ -12034.1482] [Topology ] . ( 209 sec) [ -12032.8084] [Topology ] . ( 211 sec) [ -12029.9175] [Topology ] . ( 212 sec) [ -12026.4639] [Topology ] . ( 214 sec) [ -12025.3012] [Topology ] . ( 216 sec) [ -12024.9393] [Topology ] . ( 218 sec) [ -12024.8264] [Topology ] . ( 219 sec) [ -12024.7866] [GTR parameters ] . ( 220 sec) [ -12024.7866] [Alpha ][ 0.299238] . ( 220 sec) [ -12024.7866] [Topology ] . ( 221 sec) [ -12024.7493] [Topology ] . ( 223 sec) [ -12024.7370] [Topology ] . ( 225 sec) [ -12024.7324] [Topology ] . ( 227 sec) [ -12024.7304] [Topology ] . ( 229 sec) [ -12024.7295] [Topology ] . ( 230 sec) [ -12024.7290] [GTR parameters ] . ( 230 sec) [ -12024.7290] [Alpha ][ 0.299238] . ( 230 sec) [ -12024.7290] [Topology ] . ( 232 sec) [ -12024.7284] [Topology ] . ( 232 sec) [ -12024.7284] [GTR parameters ] . ( 232 sec) [ -12024.7284] [Alpha ][ 0.299238] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12024.728415. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -38888.7747] [GTR parameters ] . ( 1 sec) [ -37915.6619] [Alpha ][ 0.500960] . ( 2 sec) [ -37054.0711] [ 5936] [depth= 9] . ( 2 sec) [ -35709.4466] [ 5838] [depth= 8] . ( 2 sec) [ -35708.7027] [ 5839] [depth= 2] . ( 2 sec) [ -35491.4088] [ 5837] [depth= 10] . ( 2 sec) [ -35429.2080] [ 5721] [depth= 10] . ( 2 sec) [ -34847.3455] [ 5715] [depth= 6] . ( 2 sec) [ -34361.2676] [ 5713] [depth= 1] . ( 2 sec) [ -34209.3720] [ 5711] [depth= 2] . ( 2 sec) [ -33847.2642] [ 5684] [depth= 3] . ( 3 sec) [ -33600.9904] [ 5681] [depth= 3] . ( 3 sec) [ -33516.0576] [ 5664] [depth= 5] . ( 3 sec) [ -33512.1138] [ 5665] [depth= 1] . ( 3 sec) [ -33430.8660] [ 5649] [depth= 4] . ( 3 sec) [ -33344.5820] [ 5649] [depth= 1] . ( 3 sec) [ -33335.1553] [ 5649] [depth= 5] . ( 3 sec) [ -33271.0921] [ 5650] [depth= 2] . ( 3 sec) [ -32569.1367] [ 5593] [depth= 12] . ( 3 sec) [ -32493.6751] [ 5596] [depth= 1] . ( 3 sec) [ -32457.6111] [ 5532] [depth= 12] . ( 4 sec) [ -32430.7892] [ 5528] [depth= 1] . ( 4 sec) [ -32393.7592] [ 5527] [depth= 8] . ( 4 sec) [ -32149.6423] [ 5490] [depth= 13] . ( 4 sec) [ -32137.2008] [ 5489] [depth= 5] . ( 4 sec) [ -32048.8741] [ 5480] [depth= 15] . ( 4 sec) [ -31271.4788] [ 5383] [depth= 12] . ( 4 sec) [ -30741.1985] [ 5258] [depth= 5] . ( 5 sec) [ -30714.9490] [ 5259] [depth= 22] . ( 5 sec) [ -30068.8270] [ 5227] [depth= 7] . ( 5 sec) [ -29946.9794] [ 5225] [depth= 5] . ( 5 sec) [ -29522.1393] [ 5181] [depth= 15] . ( 5 sec) [ -29423.8241] [ 5175] [depth= 3] . ( 5 sec) [ -29423.2520] [ 5172] [depth= 3] . ( 5 sec) [ -29420.7973] [ 5173] [depth= 2] . ( 5 sec) [ -28644.7855] [ 5123] [depth= 5] . ( 6 sec) [ -28337.0749] [ 5113] [depth= 3] . ( 6 sec) [ -28316.3376] [ 5086] [depth= 8] . ( 6 sec) [ -28296.5208] [ 5084] [depth= 3] . ( 6 sec) [ -27690.5545] [ 5034] [depth= 12] . ( 6 sec) [ -27045.8911] [ 4848] [depth= 15] . ( 6 sec) [ -26637.7675] [ 4764] [depth= 9] . ( 6 sec) [ -26570.1887] [ 4764] [depth= 1] . ( 6 sec) [ -26329.7676] [ 4764] [depth= 1] . ( 7 sec) [ -26191.9023] [ 4762] [depth= 1] . ( 7 sec) [ -26141.5005] [ 4762] [depth= 1] . ( 7 sec) [ -25881.5229] [ 4670] [depth= 14] . ( 7 sec) [ -25630.2866] [ 4594] [depth= 7] . ( 7 sec) [ -25583.4860] [ 4594] [depth= 1] . ( 7 sec) [ -25150.0702] [ 4558] [depth= 11] . ( 7 sec) [ -24857.7509] [ 4532] [depth= 10] . ( 8 sec) [ -24857.2653] [ 4588] [depth= 16] . ( 8 sec) [ -24791.0557] [ 4550] [depth= 1] . ( 8 sec) [ -24787.6749] [ 4549] [depth= 1] . ( 8 sec) [ -24629.0236] [ 4467] [depth= 8] . ( 8 sec) [ -24628.3300] [ 4467] [depth= 1] . ( 8 sec) [ -24435.4611] [ 4385] [depth= 11] . ( 9 sec) [ -24239.2773] [ 4383] [depth= 1] . ( 9 sec) [ -24215.2656] [ 4358] [depth= 7] . ( 9 sec) [ -24188.8432] [ 4340] [depth= 1] . ( 9 sec) [ -23788.0744] [ 4314] [depth= 1] . ( 9 sec) [ -23060.9504] [ 4311] [depth= 9] . ( 9 sec) [ -23028.2150] [ 4311] [depth= 1] . ( 9 sec) [ -22577.9823] [ 4253] [depth= 9] . ( 9 sec) [ -21480.3815] [ 4213] [depth= 18] . ( 10 sec) [ -21474.0817] [ 4213] [depth= 2] . ( 10 sec) [ -20258.2885] [ 4172] [depth= 14] . ( 10 sec) [ -19915.7096] [ 4084] [depth= 16] . ( 10 sec) [ -19667.0965] [ 4018] [depth= 4] . ( 10 sec) [ -19390.8012] [ 4018] [depth= 14] . ( 10 sec) [ -19336.6482] [ 3989] [depth= 14] . ( 10 sec) [ -19251.5810] [ 3953] [depth= 3] . ( 11 sec) [ -19209.0064] [ 3927] [depth= 14] . ( 11 sec) [ -19158.1402] [ 3943] [depth= 2] . ( 11 sec) [ -19117.8649] [ 3935] [depth= 13] . ( 11 sec) [ -18787.5667] [ 3830] [depth= 10] . ( 11 sec) [ -18712.4822] [ 3830] [depth= 2] . ( 11 sec) [ -18708.0873] [ 3830] [depth= 2] . ( 12 sec) [ -18681.9903] [ 3820] [depth= 10] . ( 12 sec) [ -18607.2757] [ 3811] [depth= 3] . ( 12 sec) [ -18374.2243] [ 3807] [depth= 1] . ( 12 sec) [ -18319.4441] [ 3750] [depth= 12] . ( 12 sec) [ -18125.8732] [ 3729] [depth= 1] . ( 12 sec) [ -18114.3163] [ 3730] [depth= 13] . ( 12 sec) [ -18087.5131] [ 3728] [depth= 1] . ( 12 sec) [ -18047.6674] [ 3715] [depth= 1] . ( 12 sec) [ -18013.4987] [ 3715] [depth= 2] . ( 13 sec) [ -17915.8022] [ 3712] [depth= 10] . ( 13 sec) [ -16470.7791] [ 3715] [depth= 7] . ( 13 sec) [ -16426.8909] [ 3679] [depth= 10] . ( 13 sec) [ -16394.8326] [ 3636] [depth= 11] . ( 13 sec) [ -16352.6042] [ 3609] [depth= 3] . ( 14 sec) [ -16149.6433] [ 3534] [depth= 5] . ( 14 sec) [ -16102.4257] [ 3496] [depth= 1] . ( 14 sec) [ -15962.8162] [ 3509] [depth= 6] . ( 14 sec) [ -15944.0557] [ 3500] [depth= 2] . ( 14 sec) [ -15943.3004] [ 3498] [depth= 1] . ( 14 sec) [ -15863.1106] [ 3480] [depth= 7] . ( 14 sec) [ -15855.2886] [ 3479] [depth= 2] . ( 15 sec) [ -15854.5480] [ 3479] [depth= 18] . ( 15 sec) [ -15751.5995] [ 3444] [depth= 8] . ( 15 sec) [ -15612.3127] [ 3424] [depth= 4] . ( 15 sec) [ -15611.2473] [ 3424] [depth= 9] . ( 15 sec) [ -15508.6906] [ 3424] [depth= 12] . ( 15 sec) [ -15241.6298] [ 3332] [depth= 7] . ( 15 sec) [ -15161.9897] [ 3312] [depth= 6] . ( 16 sec) [ -15146.0184] [ 3294] [depth= 4] . ( 16 sec) [ -15145.6470] [ 3294] [depth= 2] . ( 16 sec) [ -15119.5768] [ 3275] [depth= 4] . ( 16 sec) [ -15104.3116] [ 3272] [depth= 1] . ( 16 sec) [ -15067.6841] [ 3260] [depth= 5] . ( 17 sec) [ -14920.2358] [ 3233] [depth= 2] . ( 17 sec) [ -14898.4282] [ 3211] [depth= 1] . ( 17 sec) [ -14662.7524] [ 3159] [depth= 17] . ( 18 sec) [ -14660.3249] [ 3159] [depth= 6] . ( 18 sec) [ -14633.9634] [ 3152] [depth= 1] . ( 18 sec) [ -14620.5103] [ 3140] [depth= 3] . ( 18 sec) [ -14564.6671] [ 3140] [depth= 1] . ( 18 sec) [ -14563.5673] [ 3140] [depth= 2] . ( 18 sec) [ -14016.0790] [ 3072] [depth= 4] . ( 18 sec) [ -13937.0765] [ 3049] [depth= 3] . ( 18 sec) [ -13928.4508] [ 3049] [depth= 1] . ( 19 sec) [ -13927.9439] [ 3049] [depth= 6] . ( 19 sec) [ -13917.6190] [ 3049] [depth= 6] . ( 19 sec) [ -13795.1552] [ 3031] [depth= 3] . ( 19 sec) [ -13792.5754] [ 3031] [depth= 3] . ( 19 sec) [ -13791.2221] [ 3031] [depth= 3] . ( 19 sec) [ -13790.0924] [ 3031] [depth= 1] . ( 19 sec) [ -13787.8692] [ 3031] [depth= 2] . ( 20 sec) [ -13787.4579] [ 3031] [depth= 4] . ( 20 sec) [ -13667.0802] [ 2955] [depth= 18] . ( 20 sec) [ -13667.0498] [ 2955] [depth= 5] . ( 20 sec) [ -13666.8694] [ 2955] [depth= 3] . ( 20 sec) [ -13658.1940] [ 2958] [depth= 1] . ( 20 sec) [ -13592.5586] [ 2933] [depth= 2] . ( 20 sec) [ -13397.7482] [ 2929] [depth= 8] . ( 21 sec) [ -13396.9871] [ 2929] [depth= 5] . ( 21 sec) [ -13371.0860] [ 2929] [depth= 1] . ( 21 sec) [ -13363.7065] [ 2929] [depth= 11] . ( 21 sec) [ -13223.7181] [ 2895] [depth= 1] . ( 21 sec) [ -13177.6696] [ 2877] [depth= 1] . ( 21 sec) [ -13041.2274] [ 2875] [depth= 1] . ( 22 sec) [ -13012.0429] [ 2861] [depth= 15] . ( 22 sec) [ -13000.4644] [ 2861] [depth= 1] . ( 22 sec) [ -12999.6566] [ 2861] [depth= 1] . ( 22 sec) [ -12999.6333] [ 2861] [depth= 7] . ( 22 sec) [ -12999.1300] [ 2861] [depth= 4] . ( 23 sec) [ -12998.8611] [ 2861] [depth= 5] . ( 23 sec) [ -12991.1602] [ 2865] [depth= 6] . ( 23 sec) [ -12982.3123] [ 2868] [depth= 1] . ( 23 sec) [ -12978.6231] [ 2862] [depth= 4] . ( 23 sec) [ -12963.4600] [ 2856] [depth= 1] . ( 23 sec) [ -12962.2304] [ 2858] [depth= 1] . ( 23 sec) [ -12957.3119] [ 2851] [depth= 2] . ( 23 sec) [ -12951.6391] [ 2853] [depth= 2] . ( 24 sec) [ -12950.8912] [ 2852] [depth= 1] . ( 24 sec) [ -12932.2884] [ 2839] [depth= 1] . ( 25 sec) [ -12486.6075] [Branch lengths ] . ( 30 sec) [ -12305.9516] [GTR parameters ] . ( 30 sec) [ -12255.0781] [Alpha ][ 0.314859] . ( 30 sec) [ -12250.8047] [ 2837] [depth= 5] . ( 30 sec) [ -12248.3330] [ 2822] [depth= 4] . ( 31 sec) [ -12241.4792] [ 2820] [depth= 2] . ( 31 sec) [ -12220.7841] [ 2806] [depth= 1] . ( 31 sec) [ -12220.0711] [ 2799] [depth= 1] . ( 31 sec) [ -12219.9466] [ 2799] [depth= 3] . ( 32 sec) [ -12219.9325] [ 2799] [depth= 4] . ( 33 sec) [ -12219.9155] [ 2799] [depth= 7] . ( 33 sec) [ -12212.1829] [ 2795] [depth= 1] . ( 33 sec) [ -12212.1656] [ 2795] [depth= 1] . ( 33 sec) [ -12212.1370] [ 2799] [depth= 1] . ( 35 sec) [ -12212.1241] [ 2799] [depth= 5] . ( 35 sec) [ -12212.0725] [ 2799] [depth= 11] . ( 35 sec) [ -12203.4870] [ 2796] [depth= 2] . ( 36 sec) [ -12198.2275] [ 2795] [depth= 6] . ( 36 sec) [ -12172.5122] [ 2768] [depth= 1] . ( 36 sec) [ -12165.8555] [ 2768] [depth= 1] . ( 37 sec) [ -12165.2388] [ 2768] [depth= 1] . ( 37 sec) [ -12165.1507] [ 2768] [depth= 1] . ( 37 sec) [ -12165.1390] [ 2768] [depth= 9] . ( 38 sec) [ -12165.1045] [ 2767] [depth= 1] . ( 38 sec) [ -12161.4154] [ 2768] [depth= 1] . ( 39 sec) [ -12154.9445] [ 2764] [depth= 3] . ( 40 sec) [ -12154.9035] [ 2764] [depth= 1] . ( 40 sec) [ -12114.2144] [ 2718] [depth= 7] . ( 41 sec) [ -12110.6337] [ 2711] [depth= 1] . ( 41 sec) [ -12095.3899] [ 2703] [depth= 1] . ( 42 sec) [ -12093.4808] [ 2703] [depth= 1] . ( 42 sec) [ -12093.4699] [ 2703] [depth= 5] . ( 44 sec) [ -12092.5086] [ 2699] [depth= 1] . ( 45 sec) [ -12086.4095] [ 2696] [depth= 2] . ( 49 sec) [ -12074.1584] [ 2680] [depth= 6] . ( 52 sec) [ -12073.7252] [ 2680] [depth= 1] . ( 52 sec) [ -12073.6510] [ 2680] [depth= 3] . ( 53 sec) [ -12072.7009] [ 2682] [depth= 2] . ( 53 sec) [ -12072.6899] [ 2682] [depth= 1] . ( 55 sec) [ -12072.6658] [ 2682] [depth= 1] . ( 56 sec) [ -12072.6375] [ 2682] [depth= 1] . ( 57 sec) [ -12072.5819] [ 2682] [depth= 1] . ( 59 sec) [ -12072.1412] [ 2687] [depth= 1] . ( 60 sec) [ -12037.1104] [Branch lengths ] . ( 65 sec) [ -12032.5453] [GTR parameters ] . ( 65 sec) [ -12032.1681] [Alpha ][ 0.302716] . ( 65 sec) [ -12031.2223] [ 2686] [depth= 1] . ( 71 sec) [ -12031.2034] [ 2686] [depth= 5] . ( 75 sec) [ -12030.7443] [ 2685] [depth= 1] . ( 75 sec) [ -12029.7576] [ 2683] [depth= 1] . ( 79 sec) [ -12029.7398] [ 2683] [depth= 1] . ( 81 sec) [ -12029.3086] [ 2681] [depth= 1] . ( 81 sec) [ -12028.7256] [ 2683] [depth= 1] . ( 90 sec) [ -12028.5932] [ 2683] [depth= 6] . ( 98 sec) [ -12025.1496] [Branch lengths ] . ( 105 sec) [ -12025.0408] [GTR parameters ] . ( 105 sec) [ -12025.0181] [Alpha ][ 0.299697] . ( 106 sec) [ -12024.7838] [ 2687] [depth= 2] . ( 137 sec) [ -12024.0517] [Branch lengths ] . ( 140 sec) [ -12024.0368] [GTR parameters ] . ( 140 sec) [ -12024.0366] [Alpha ][ 0.299352] . ( 162 sec) [ -12023.8348] [ 2683] [depth= 2] . ( 216 sec) [ -12022.9665] [Branch lengths ] . ( 223 sec) [ -12022.9334] [GTR parameters ] . ( 223 sec) [ -12022.9142] [Alpha ][ 0.301999] . ( 300 sec) [ -12022.7712] [Branch lengths ] . ( 300 sec) [ -12022.7712] [Topology ] . ( 302 sec) [ -12022.7267] [Topology ] . ( 304 sec) [ -12022.6994] [Topology ] . ( 306 sec) [ -12022.6914] [Topology ] . ( 308 sec) [ -12022.6883] [Topology ] . ( 309 sec) [ -12022.6870] [Topology ] . ( 311 sec) [ -12022.6864] [Topology ] . ( 316 sec) [ -12022.6834] [GTR parameters ] . ( 316 sec) [ -12022.6834] [Alpha ][ 0.301999] . ( 316 sec) [ -12022.6834] [Topology ] . ( 318 sec) [ -12022.6824] [Topology ] . ( 319 sec) [ -12022.6821] [GTR parameters ] . ( 320 sec) [ -12022.6821] [Alpha ][ 0.301697] . ( 320 sec) [ -12022.6821] [Topology ] . ( 321 sec) [ -12022.6814] [Topology ] . ( 324 sec) [ -12022.6812] [GTR parameters ] . ( 324 sec) [ -12022.6812] [Alpha ][ 0.301697] . Checking for NNIs, optimizing five branches... . ( 338 sec) [ -12022.6811] [Topology ] . Checking for NNIs, optimizing five branches... . ( 352 sec) [ -12022.6808] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12022.680838. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -42734.8750] [GTR parameters ] . ( 1 sec) [ -41634.2867] [Alpha ][ 0.500960] . ( 2 sec) [ -40456.5873] [ 6166] [depth= 8] . ( 2 sec) [ -38575.5020] [ 6096] [depth= 10] . ( 2 sec) [ -38235.2013] [ 6069] [depth= 7] . ( 2 sec) [ -37835.9976] [ 6048] [depth= 1] . ( 2 sec) [ -37090.9670] [ 6004] [depth= 3] . ( 2 sec) [ -36645.0058] [ 5925] [depth= 2] . ( 2 sec) [ -36207.3298] [ 5918] [depth= 8] . ( 2 sec) [ -36017.6406] [ 5876] [depth= 1] . ( 2 sec) [ -35404.4119] [ 5863] [depth= 8] . ( 3 sec) [ -34400.8737] [ 5849] [depth= 4] . ( 3 sec) [ -34309.9300] [ 5834] [depth= 9] . ( 3 sec) [ -34232.6338] [ 5826] [depth= 1] . ( 3 sec) [ -34136.4781] [ 5825] [depth= 7] . ( 3 sec) [ -33439.3957] [ 5813] [depth= 2] . ( 3 sec) [ -33188.2050] [ 5801] [depth= 5] . ( 3 sec) [ -32812.0812] [ 5778] [depth= 7] . ( 3 sec) [ -32309.2859] [ 5672] [depth= 8] . ( 4 sec) [ -32188.7740] [ 5653] [depth= 1] . ( 4 sec) [ -32031.2984] [ 5636] [depth= 11] . ( 4 sec) [ -31882.9198] [ 5609] [depth= 4] . ( 4 sec) [ -31649.6051] [ 5610] [depth= 3] . ( 4 sec) [ -31336.0379] [ 5594] [depth= 18] . ( 4 sec) [ -31261.5368] [ 5589] [depth= 1] . ( 4 sec) [ -31254.6681] [ 5587] [depth= 1] . ( 4 sec) [ -30226.6945] [ 5587] [depth= 8] . ( 5 sec) [ -30132.5519] [ 5484] [depth= 9] . ( 5 sec) [ -30111.8629] [ 5483] [depth= 6] . ( 5 sec) [ -29961.7492] [ 5479] [depth= 1] . ( 5 sec) [ -29925.1438] [ 5477] [depth= 6] . ( 5 sec) [ -29835.1186] [ 5460] [depth= 14] . ( 5 sec) [ -29731.3716] [ 5439] [depth= 6] . ( 5 sec) [ -29588.0904] [ 5434] [depth= 8] . ( 5 sec) [ -29518.5011] [ 5426] [depth= 5] . ( 5 sec) [ -28300.3505] [ 5372] [depth= 14] . ( 6 sec) [ -27463.2088] [ 5372] [depth= 1] . ( 6 sec) [ -27074.2150] [ 5421] [depth= 1] . ( 6 sec) [ -26555.5619] [ 5377] [depth= 19] . ( 6 sec) [ -26537.0407] [ 5278] [depth= 21] . ( 6 sec) [ -26066.7884] [ 5206] [depth= 21] . ( 6 sec) [ -25670.1096] [ 5133] [depth= 3] . ( 6 sec) [ -25520.6087] [ 5063] [depth= 21] . ( 6 sec) [ -25302.4308] [ 5029] [depth= 2] . ( 7 sec) [ -25125.4929] [ 5002] [depth= 16] . ( 7 sec) [ -25103.1531] [ 5002] [depth= 10] . ( 7 sec) [ -24420.7306] [ 4776] [depth= 11] . ( 7 sec) [ -24388.8386] [ 4776] [depth= 9] . ( 7 sec) [ -24383.4452] [ 4778] [depth= 1] . ( 7 sec) [ -23904.8852] [ 4768] [depth= 1] . ( 7 sec) [ -23487.4981] [ 4760] [depth= 3] . ( 7 sec) [ -23418.4575] [ 4738] [depth= 13] . ( 8 sec) [ -23173.4980] [ 4619] [depth= 21] . ( 8 sec) [ -22913.6413] [ 4612] [depth= 11] . ( 8 sec) [ -22277.8107] [ 4575] [depth= 5] . ( 8 sec) [ -21423.7436] [ 4569] [depth= 4] . ( 8 sec) [ -21320.8831] [ 4572] [depth= 1] . ( 8 sec) [ -21251.6856] [ 4567] [depth= 13] . ( 8 sec) [ -20936.2153] [ 4497] [depth= 16] . ( 8 sec) [ -20932.2580] [ 4497] [depth= 12] . ( 9 sec) [ -20928.1281] [ 4497] [depth= 24] . ( 9 sec) [ -20875.3387] [ 4474] [depth= 11] . ( 9 sec) [ -20761.6709] [ 4388] [depth= 19] . ( 9 sec) [ -20658.0821] [ 4391] [depth= 1] . ( 9 sec) [ -20609.8807] [ 4351] [depth= 18] . ( 9 sec) [ -20607.0924] [ 4351] [depth= 3] . ( 9 sec) [ -20529.7575] [ 4319] [depth= 3] . ( 9 sec) [ -20154.1972] [ 4214] [depth= 6] . ( 10 sec) [ -19942.6639] [ 4152] [depth= 11] . ( 10 sec) [ -19884.4821] [ 4150] [depth= 1] . ( 10 sec) [ -19865.8769] [ 4151] [depth= 7] . ( 10 sec) [ -19416.8218] [ 4113] [depth= 6] . ( 10 sec) [ -19354.6753] [ 4048] [depth= 13] . ( 10 sec) [ -19242.3324] [ 4021] [depth= 3] . ( 10 sec) [ -19201.9937] [ 4004] [depth= 19] . ( 10 sec) [ -19014.2032] [ 3980] [depth= 3] . ( 11 sec) [ -18977.3978] [ 3980] [depth= 1] . ( 11 sec) [ -18853.0547] [ 3974] [depth= 3] . ( 11 sec) [ -18853.0255] [ 3974] [depth= 1] . ( 11 sec) [ -18818.9534] [ 3950] [depth= 14] . ( 11 sec) [ -18818.9375] [ 3950] [depth= 1] . ( 11 sec) [ -18513.3994] [ 3806] [depth= 10] . ( 11 sec) [ -18423.7266] [ 3794] [depth= 3] . ( 11 sec) [ -18297.5045] [ 3796] [depth= 1] . ( 12 sec) [ -18286.3115] [ 3796] [depth= 5] . ( 12 sec) [ -17959.7935] [ 3720] [depth= 17] . ( 12 sec) [ -17770.0668] [ 3679] [depth= 1] . ( 12 sec) [ -17733.4097] [ 3679] [depth= 2] . ( 12 sec) [ -17584.6258] [ 3561] [depth= 5] . ( 12 sec) [ -17293.8876] [ 3513] [depth= 2] . ( 12 sec) [ -17180.7239] [ 3498] [depth= 3] . ( 12 sec) [ -17154.4712] [ 3499] [depth= 6] . ( 13 sec) [ -17147.4034] [ 3498] [depth= 6] . ( 13 sec) [ -16906.8551] [ 3423] [depth= 22] . ( 13 sec) [ -16804.5570] [ 3423] [depth= 1] . ( 13 sec) [ -16800.7195] [ 3423] [depth= 1] . ( 13 sec) [ -16761.2273] [ 3423] [depth= 2] . ( 13 sec) [ -16744.2475] [ 3423] [depth= 1] . ( 13 sec) [ -16642.6772] [ 3398] [depth= 1] . ( 13 sec) [ -16585.6326] [ 3376] [depth= 1] . ( 14 sec) [ -16323.0078] [ 3364] [depth= 12] . ( 14 sec) [ -16303.8586] [ 3359] [depth= 2] . ( 14 sec) [ -16288.0193] [ 3359] [depth= 1] . ( 14 sec) [ -16049.4374] [ 3315] [depth= 5] . ( 14 sec) [ -16013.8908] [ 3315] [depth= 2] . ( 14 sec) [ -15716.3929] [ 3232] [depth= 20] . ( 14 sec) [ -15555.4704] [ 3192] [depth= 12] . ( 15 sec) [ -15539.2604] [ 3192] [depth= 1] . ( 15 sec) [ -15530.1477] [ 3192] [depth= 14] . ( 15 sec) [ -15505.7399] [ 3193] [depth= 1] . ( 15 sec) [ -15505.2712] [ 3193] [depth= 6] . ( 15 sec) [ -15492.7986] [ 3196] [depth= 1] . ( 15 sec) [ -15492.2925] [ 3196] [depth= 1] . ( 15 sec) [ -15486.9639] [ 3197] [depth= 2] . ( 15 sec) [ -15455.2246] [ 3197] [depth= 1] . ( 16 sec) [ -15406.3147] [ 3177] [depth= 4] . ( 16 sec) [ -14881.3780] [ 3166] [depth= 2] . ( 16 sec) [ -14825.0203] [ 3161] [depth= 1] . ( 16 sec) [ -14754.9731] [ 3136] [depth= 2] . ( 16 sec) [ -14555.7326] [ 3111] [depth= 11] . ( 16 sec) [ -14469.2856] [ 3083] [depth= 5] . ( 16 sec) [ -14451.5122] [ 3088] [depth= 4] . ( 16 sec) [ -14430.7302] [ 3088] [depth= 1] . ( 17 sec) [ -14198.7183] [ 3061] [depth= 1] . ( 17 sec) [ -14168.6699] [ 3045] [depth= 10] . ( 17 sec) [ -14163.8228] [ 3047] [depth= 1] . ( 17 sec) [ -14163.1630] [ 3047] [depth= 1] . ( 17 sec) [ -14012.2810] [ 3024] [depth= 4] . ( 17 sec) [ -13905.3549] [ 3012] [depth= 1] . ( 17 sec) [ -13834.9258] [ 3015] [depth= 1] . ( 17 sec) [ -13818.1308] [ 3015] [depth= 1] . ( 18 sec) [ -13817.3420] [ 3015] [depth= 5] . ( 18 sec) [ -13816.4784] [ 3015] [depth= 8] . ( 18 sec) [ -13813.3677] [ 3014] [depth= 1] . ( 18 sec) [ -13699.3947] [ 2952] [depth= 2] . ( 19 sec) [ -13576.3309] [ 2917] [depth= 4] . ( 19 sec) [ -13576.0453] [ 2917] [depth= 5] . ( 19 sec) [ -13547.6857] [ 2905] [depth= 6] . ( 19 sec) [ -13231.7566] [ 2864] [depth= 1] . ( 19 sec) [ -13165.2181] [ 2831] [depth= 3] . ( 19 sec) [ -13160.3296] [ 2824] [depth= 1] . ( 19 sec) [ -13143.3453] [ 2818] [depth= 1] . ( 19 sec) [ -13141.1559] [ 2818] [depth= 1] . ( 20 sec) [ -13009.5633] [ 2787] [depth= 5] . ( 20 sec) [ -12890.9154] [ 2787] [depth= 10] . ( 20 sec) [ -12888.5145] [ 2787] [depth= 10] . ( 20 sec) [ -12887.8648] [ 2787] [depth= 10] . ( 20 sec) [ -12869.3243] [ 2783] [depth= 1] . ( 20 sec) [ -12860.1428] [ 2779] [depth= 3] . ( 20 sec) [ -12851.2127] [ 2773] [depth= 1] . ( 20 sec) [ -12833.4682] [ 2762] [depth= 2] . ( 21 sec) [ -12807.5522] [ 2766] [depth= 1] . ( 21 sec) [ -12802.3339] [ 2766] [depth= 1] . ( 21 sec) [ -12802.3212] [ 2766] [depth= 9] . ( 21 sec) [ -12801.7923] [ 2766] [depth= 5] . ( 21 sec) [ -12801.7141] [ 2766] [depth= 8] . ( 21 sec) [ -12756.0339] [ 2768] [depth= 2] . ( 21 sec) [ -12641.2533] [ 2774] [depth= 1] . ( 22 sec) [ -12594.3790] [ 2750] [depth= 9] . ( 22 sec) [ -12585.8385] [ 2750] [depth= 1] . ( 22 sec) [ -12585.4370] [ 2750] [depth= 1] . ( 23 sec) [ -12354.4183] [Branch lengths ] . ( 26 sec) [ -12244.7651] [GTR parameters ] . ( 27 sec) [ -12199.5562] [Alpha ][ 0.321781] . ( 27 sec) [ -12196.2827] [ 2749] [depth= 1] . ( 27 sec) [ -12194.5341] [ 2748] [depth= 6] . ( 27 sec) [ -12185.0090] [ 2746] [depth= 1] . ( 27 sec) [ -12183.7945] [ 2748] [depth= 1] . ( 28 sec) [ -12183.7404] [ 2748] [depth= 3] . ( 28 sec) [ -12183.5333] [ 2748] [depth= 1] . ( 28 sec) [ -12183.4482] [ 2748] [depth= 1] . ( 28 sec) [ -12172.3664] [ 2744] [depth= 1] . ( 29 sec) [ -12162.0052] [ 2732] [depth= 4] . ( 29 sec) [ -12161.9675] [ 2732] [depth= 3] . ( 30 sec) [ -12161.9504] [ 2732] [depth= 5] . ( 30 sec) [ -12161.9351] [ 2732] [depth= 9] . ( 31 sec) [ -12161.8997] [ 2732] [depth= 1] . ( 31 sec) [ -12161.2708] [ 2732] [depth= 1] . ( 32 sec) [ -12139.0203] [ 2715] [depth= 1] . ( 32 sec) [ -12139.0096] [ 2715] [depth= 2] . ( 32 sec) [ -12121.4605] [ 2711] [depth= 1] . ( 33 sec) [ -12121.4198] [ 2711] [depth= 1] . ( 34 sec) [ -12121.3932] [ 2709] [depth= 2] . ( 34 sec) [ -12113.6328] [ 2708] [depth= 2] . ( 37 sec) [ -12113.4846] [ 2708] [depth= 1] . ( 37 sec) [ -12111.7990] [ 2702] [depth= 2] . ( 38 sec) [ -12106.9737] [ 2702] [depth= 1] . ( 39 sec) [ -12106.8611] [ 2702] [depth= 1] . ( 39 sec) [ -12106.7896] [ 2702] [depth= 1] . ( 39 sec) [ -12104.7723] [ 2702] [depth= 1] . ( 39 sec) [ -12102.2458] [ 2697] [depth= 1] . ( 40 sec) [ -12101.4756] [ 2697] [depth= 1] . ( 41 sec) [ -12101.4294] [ 2697] [depth= 1] . ( 41 sec) [ -12100.3562] [ 2697] [depth= 1] . ( 43 sec) [ -12097.5225] [ 2696] [depth= 1] . ( 43 sec) [ -12093.3884] [ 2693] [depth= 1] . ( 44 sec) [ -12092.9650] [ 2693] [depth= 1] . ( 44 sec) [ -12090.8700] [ 2692] [depth= 3] . ( 45 sec) [ -12087.6791] [ 2692] [depth= 1] . ( 45 sec) [ -12087.6201] [ 2692] [depth= 1] . ( 46 sec) [ -12087.6097] [ 2692] [depth= 3] . ( 46 sec) [ -12087.5618] [ 2693] [depth= 1] . ( 46 sec) [ -12084.4044] [ 2693] [depth= 1] . ( 47 sec) [ -12084.2611] [ 2693] [depth= 1] . ( 47 sec) [ -12083.4152] [ 2697] [depth= 1] . ( 47 sec) [ -12082.7023] [ 2698] [depth= 1] . ( 48 sec) [ -12081.0837] [ 2694] [depth= 2] . ( 51 sec) [ -12069.9932] [ 2685] [depth= 2] . ( 51 sec) [ -12069.7204] [ 2686] [depth= 1] . ( 53 sec) [ -12069.6799] [ 2686] [depth= 10] . ( 53 sec) [ -12068.7870] [ 2677] [depth= 1] . ( 53 sec) [ -12066.2341] [ 2682] [depth= 1] . ( 54 sec) [ -12065.8826] [ 2682] [depth= 3] . ( 56 sec) [ -12044.2867] [Branch lengths ] . ( 58 sec) [ -12041.3321] [GTR parameters ] . ( 58 sec) [ -12040.8021] [Alpha ][ 0.307069] . ( 59 sec) [ -12038.8272] [ 2676] [depth= 1] . ( 60 sec) [ -12037.5901] [ 2680] [depth= 1] . ( 62 sec) [ -12036.1383] [ 2678] [depth= 1] . ( 65 sec) [ -12036.1132] [ 2678] [depth= 1] . ( 69 sec) [ -12036.0049] [ 2672] [depth= 1] . ( 71 sec) [ -12035.9921] [ 2672] [depth= 5] . ( 73 sec) [ -12035.2038] [ 2678] [depth= 1] . ( 74 sec) [ -12035.1901] [ 2678] [depth= 1] . ( 75 sec) [ -12035.1532] [ 2678] [depth= 1] . ( 80 sec) [ -12034.3477] [ 2675] [depth= 1] . ( 90 sec) [ -12034.0909] [ 2676] [depth= 1] . ( 91 sec) [ -12028.9868] [Branch lengths ] . ( 93 sec) [ -12028.7729] [GTR parameters ] . ( 93 sec) [ -12028.7641] [Alpha ][ 0.305164] . ( 93 sec) [ -12028.4821] [ 2681] [depth= 2] . ( 123 sec) [ -12027.8820] [ 2680] [depth= 1] . ( 124 sec) [ -12026.3134] [Branch lengths ] . ( 126 sec) [ -12026.2828] [GTR parameters ] . ( 126 sec) [ -12026.2774] [Alpha ][ 0.303663] . ( 158 sec) [ -12025.8213] [Branch lengths ] . ( 235 sec) [ -12025.5778] [Branch lengths ] . ( 235 sec) [ -12025.5778] [Topology ] . ( 237 sec) [ -12025.2911] [Topology ] . ( 239 sec) [ -12024.4575] [Topology ] . ( 241 sec) [ -12024.0438] [Topology ] . ( 243 sec) [ -12023.9846] [Topology ] . ( 244 sec) [ -12023.9717] [Topology ] . ( 246 sec) [ -12023.9682] [Topology ] . ( 248 sec) [ -12023.9469] [GTR parameters ] . ( 248 sec) [ -12023.9434] [Alpha ][ 0.302456] . ( 248 sec) [ -12023.9434] [Topology ] . ( 250 sec) [ -12023.9387] [Topology ] . ( 252 sec) [ -12023.9371] [Topology ] . ( 253 sec) [ -12023.9363] [Topology ] . ( 254 sec) [ -12023.9350] [GTR parameters ] . ( 255 sec) [ -12023.9349] [Alpha ][ 0.302153] . ( 255 sec) [ -12023.9349] [Topology ] . ( 256 sec) [ -12023.9339] [Topology ] . ( 257 sec) [ -12023.9338] [GTR parameters ] . ( 257 sec) [ -12023.9338] [Alpha ][ 0.302153] . ( 257 sec) [ -12023.9338] [Topology ] . ( 259 sec) [ -12023.9332] [Topology ] . ( 260 sec) [ -12023.9332] [GTR parameters ] . ( 260 sec) [ -12023.9332] [Alpha ][ 0.302153] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12023.933174. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -12703.7048] [GTR parameters ] . ( 5 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 5 sec) [ -12506.3721] [Topology ] . ( 8 sec) [ -12215.6080] [Topology ] . ( 10 sec) [ -12152.0977] [Topology ] . ( 12 sec) [ -12139.1352] [Topology ] . ( 14 sec) [ -12126.7129] [Topology ] . ( 16 sec) [ -12130.9985] [Topology ] . Moving backward . ( 16 sec) [ -12121.4353] [Topology ] . ( 18 sec) [ -12122.7329] [Topology ] . Moving backward . ( 18 sec) [ -12118.4950] [Topology ] . ( 20 sec) [ -12116.6881] [Topology ] . ( 24 sec) [ -12094.3714] [GTR parameters ] . ( 24 sec) [ -12054.0715] [Alpha ][ 0.324674] . ( 24 sec) [ -12054.0715] [Topology ] . ( 26 sec) [ -12046.5550] [Topology ] . ( 28 sec) [ -12049.9254] [Topology ] . Moving backward . ( 28 sec) [ -12041.0508] [Topology ] . ( 30 sec) [ -12039.5299] [Topology ] . ( 32 sec) [ -12040.3282] [Topology ] . Moving backward . ( 32 sec) [ -12035.7717] [Topology ] . ( 34 sec) [ -12034.7699] [Topology ] . ( 35 sec) [ -12034.6451] [Topology ] . ( 37 sec) [ -12034.0025] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -12034.0255] [Topology ] . ( 56 sec) [ -12030.5971] [GTR parameters ] . ( 56 sec) [ -12029.8024] [Alpha ][ 0.306568] . ( 56 sec) [ -12029.8024] [Topology ] . ( 58 sec) [ -12029.0738] [Topology ] . ( 60 sec) [ -12029.0786] [Topology ] . Moving backward . ( 60 sec) [ -12028.8782] [Topology ] . ( 62 sec) [ -12028.8209] [Topology ] . ( 64 sec) [ -12029.0361] [Topology ] . Moving backward . ( 64 sec) [ -12028.6691] [Topology ] . ( 66 sec) [ -12028.6702] [Topology ] . Moving backward . ( 66 sec) [ -12028.5546] [Topology ] . ( 68 sec) [ -12028.4954] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -12028.4944] [Topology ] . ( 84 sec) [ -12028.2370] [GTR parameters ] . ( 84 sec) [ -12028.1961] [Alpha ][ 0.302803] . ( 84 sec) [ -12028.1961] [Topology ] . ( 86 sec) [ -12028.0997] [Topology ] . ( 88 sec) [ -12028.1125] [Topology ] . Moving backward . ( 88 sec) [ -12028.0660] [Topology ] . ( 90 sec) [ -12028.1322] [Topology ] . Moving backward . ( 90 sec) [ -12028.0427] [Topology ] . ( 92 sec) [ -12028.0742] [Topology ] . Moving backward . ( 92 sec) [ -12028.0259] [Topology ] . ( 94 sec) [ -12028.1259] [Topology ] . Moving backward . ( 94 sec) [ -12028.0120] [Topology ] . Checking for NNIs, optimizing five branches... . ( 111 sec) [ -12028.0710] [Topology ] . ( 112 sec) [ -12028.0401] [GTR parameters ] . ( 112 sec) [ -12028.0365] [Alpha ][ 0.301588] . ( 113 sec) [ -12028.0365] [Topology ] . ( 114 sec) [ -12028.0205] [Topology ] . ( 116 sec) [ -12028.4083] [Topology ] . Moving backward . ( 116 sec) [ -12027.9769] [Topology ] . ( 118 sec) [ -12028.0037] [Topology ] . Moving backward . ( 118 sec) [ -12027.8763] [Topology ] . ( 120 sec) [ -12027.8675] [Topology ] . ( 122 sec) [ -12027.9072] [Topology ] . Moving backward . ( 122 sec) [ -12027.8644] [Topology ] . ( 124 sec) [ -12027.9897] [Topology ] . Checking for NNIs, optimizing five branches... . ( 139 sec) [ -12027.8083] [Topology ] . ( 140 sec) [ -12027.8011] [GTR parameters ] . ( 141 sec) [ -12027.8005] [Alpha ][ 0.301093] . ( 141 sec) [ -12027.8005] [Topology ] . ( 142 sec) [ -12027.7950] [Topology ] . ( 144 sec) [ -12027.8067] [Topology ] . Moving backward . ( 144 sec) [ -12027.7946] [Topology ] . Checking for NNIs, optimizing five branches... . ( 159 sec) [ -12027.7925] [Topology ] . ( 160 sec) [ -12027.7921] [GTR parameters ] . ( 160 sec) [ -12027.7921] [Alpha ][ 0.301093] . ( 160 sec) [ -12027.7921] [Topology ] . ( 162 sec) [ -12027.7894] [Topology ] . ( 164 sec) [ -12027.7894] [Topology ] . Checking for NNIs, optimizing five branches... . ( 178 sec) [ -12027.7807] [Topology ] . ( 179 sec) [ -12027.7806] [GTR parameters ] . ( 179 sec) [ -12027.7806] [Alpha ][ 0.301093] . ( 179 sec) [ -12027.7806] [Topology ] . ( 181 sec) [ -12027.7797] [Topology ] . Checking for NNIs, optimizing five branches... . ( 195 sec) [ -12027.7796] [Topology ] . ( 195 sec) [ -12027.7796] [GTR parameters ] . ( 196 sec) [ -12027.7796] [Alpha ][ 0.301093] . ( 196 sec) [ -12027.7796] [Topology ] . ( 197 sec) [ -12027.7790] [Topology ] . Checking for NNIs, optimizing five branches... . ( 212 sec) [ -12027.7789] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 231 sec) [ -12703.7048] [GTR parameters ] . ( 231 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 232 sec) [ -12504.9636] [ 2715] [depth= 1] . ( 232 sec) [ -12504.7654] [ 2715] [depth= 1] . ( 232 sec) [ -12497.1136] [ 2715] [depth= 1] . ( 232 sec) [ -12493.5302] [ 2715] [depth= 1] . ( 232 sec) [ -12491.3616] [ 2715] [depth= 1] . ( 232 sec) [ -12483.4602] [ 2713] [depth= 2] . ( 233 sec) [ -12482.5118] [ 2713] [depth= 1] . ( 233 sec) [ -12482.4575] [ 2713] [depth= 1] . ( 233 sec) [ -12470.4830] [ 2713] [depth= 1] . ( 233 sec) [ -12466.0686] [ 2713] [depth= 1] . ( 233 sec) [ -12465.9179] [ 2713] [depth= 1] . ( 233 sec) [ -12449.2031] [ 2705] [depth= 1] . ( 233 sec) [ -12449.1587] [ 2705] [depth= 1] . ( 234 sec) [ -12437.2290] [ 2704] [depth= 1] . ( 234 sec) [ -12432.0204] [ 2705] [depth= 1] . ( 234 sec) [ -12431.2264] [ 2705] [depth= 1] . ( 234 sec) [ -12431.1803] [ 2705] [depth= 1] . ( 234 sec) [ -12414.3902] [ 2705] [depth= 1] . ( 235 sec) [ -12397.8831] [ 2704] [depth= 1] . ( 235 sec) [ -12388.4419] [ 2704] [depth= 1] . ( 236 sec) [ -12357.7085] [ 2703] [depth= 4] . ( 236 sec) [ -12340.0539] [ 2692] [depth= 4] . ( 236 sec) [ -12337.3933] [ 2693] [depth= 1] . ( 236 sec) [ -12290.3349] [ 2697] [depth= 1] . ( 236 sec) [ -12276.7111] [ 2700] [depth= 1] . ( 236 sec) [ -12275.6885] [ 2702] [depth= 2] . ( 236 sec) [ -12275.1313] [ 2706] [depth= 1] . ( 237 sec) [ -12274.3385] [ 2703] [depth= 1] . ( 237 sec) [ -12272.9383] [ 2701] [depth= 1] . ( 237 sec) [ -12266.5292] [ 2692] [depth= 2] . ( 237 sec) [ -12256.4860] [ 2690] [depth= 2] . ( 238 sec) [ -12252.4458] [ 2688] [depth= 1] . ( 238 sec) [ -12248.8610] [ 2682] [depth= 2] . ( 238 sec) [ -12248.1344] [ 2687] [depth= 2] . ( 238 sec) [ -12246.6557] [ 2687] [depth= 1] . ( 239 sec) [ -12246.3006] [ 2689] [depth= 1] . ( 239 sec) [ -12217.8872] [ 2684] [depth= 1] . ( 240 sec) [ -12209.5068] [ 2684] [depth= 1] . ( 240 sec) [ -12207.6577] [ 2684] [depth= 1] . ( 240 sec) [ -12207.6325] [ 2684] [depth= 2] . ( 241 sec) [ -12207.0453] [ 2684] [depth= 1] . ( 241 sec) [ -12206.9176] [ 2684] [depth= 1] . ( 241 sec) [ -12206.6771] [ 2684] [depth= 1] . ( 246 sec) [ -12205.6860] [ 2684] [depth= 1] . ( 246 sec) [ -12203.4087] [ 2684] [depth= 1] . ( 246 sec) [ -12203.3920] [ 2684] [depth= 6] . ( 247 sec) [ -12203.3687] [ 2684] [depth= 7] . ( 248 sec) [ -12198.4249] [ 2685] [depth= 9] . ( 248 sec) [ -12194.4738] [ 2684] [depth= 9] . ( 248 sec) [ -12192.8649] [ 2683] [depth= 3] . ( 248 sec) [ -12191.5426] [ 2683] [depth= 3] . ( 249 sec) [ -12191.0843] [ 2683] [depth= 1] . ( 249 sec) [ -12190.8974] [ 2683] [depth= 1] . ( 249 sec) [ -12190.8719] [ 2683] [depth= 2] . ( 250 sec) [ -12190.8488] [ 2683] [depth= 6] . ( 250 sec) [ -12190.8090] [ 2683] [depth= 6] . ( 250 sec) [ -12190.7862] [ 2683] [depth= 3] . ( 260 sec) [ -12121.2317] [Branch lengths ] . ( 263 sec) [ -12102.7305] [GTR parameters ] . ( 263 sec) [ -12064.9048] [Alpha ][ 0.326790] . ( 265 sec) [ -12064.8902] [ 2683] [depth= 1] . ( 265 sec) [ -12064.7775] [ 2680] [depth= 2] . ( 265 sec) [ -12064.2603] [ 2684] [depth= 2] . ( 266 sec) [ -12064.2338] [ 2684] [depth= 1] . ( 266 sec) [ -12060.1695] [ 2683] [depth= 1] . ( 267 sec) [ -12057.9052] [ 2680] [depth= 2] . ( 267 sec) [ -12052.4725] [ 2683] [depth= 3] . ( 269 sec) [ -12050.5920] [ 2678] [depth= 1] . ( 279 sec) [ -12050.5800] [ 2678] [depth= 1] . ( 279 sec) [ -12050.5672] [ 2678] [depth= 1] . ( 295 sec) [ -12040.1040] [Branch lengths ] . ( 298 sec) [ -12035.8716] [GTR parameters ] . ( 298 sec) [ -12035.2488] [Alpha ][ 0.310434] . ( 300 sec) [ -12035.1353] [ 2678] [depth= 1] . ( 303 sec) [ -12035.0962] [ 2678] [depth= 1] . ( 303 sec) [ -12034.2176] [ 2683] [depth= 2] . ( 315 sec) [ -12034.2061] [ 2683] [depth= 9] . ( 329 sec) [ -12030.7991] [Branch lengths ] . ( 332 sec) [ -12030.3420] [GTR parameters ] . ( 333 sec) [ -12030.3032] [Alpha ][ 0.306697] . ( 334 sec) [ -12030.2795] [ 2683] [depth= 1] . ( 364 sec) [ -12029.0319] [Branch lengths ] . ( 366 sec) [ -12028.9324] [GTR parameters ] . ( 367 sec) [ -12028.9229] [Alpha ][ 0.304719] . ( 398 sec) [ -12028.3656] [Branch lengths ] . ( 474 sec) [ -12027.5935] [Branch lengths ] . ( 474 sec) [ -12027.5935] [Topology ] . ( 476 sec) [ -12026.0225] [Topology ] . ( 478 sec) [ -12023.9745] [Topology ] . ( 480 sec) [ -12023.2568] [Topology ] . ( 481 sec) [ -12023.0084] [Topology ] . ( 483 sec) [ -12022.9239] [Topology ] . ( 485 sec) [ -12022.8906] [Topology ] . ( 486 sec) [ -12022.7514] [GTR parameters ] . ( 486 sec) [ -12022.7392] [Alpha ][ 0.302503] . ( 486 sec) [ -12022.7392] [Topology ] . ( 488 sec) [ -12022.7114] [Topology ] . ( 490 sec) [ -12022.7006] [Topology ] . ( 492 sec) [ -12022.6955] [Topology ] . ( 494 sec) [ -12022.6929] [Topology ] . ( 495 sec) [ -12022.6916] [Topology ] . ( 497 sec) [ -12022.6909] [Topology ] . ( 499 sec) [ -12022.6850] [GTR parameters ] . ( 499 sec) [ -12022.6842] [Alpha ][ 0.301899] . ( 499 sec) [ -12022.6842] [Topology ] . ( 501 sec) [ -12022.6823] [Topology ] . ( 502 sec) [ -12022.6814] [Topology ] . ( 503 sec) [ -12022.6810] [GTR parameters ] . ( 503 sec) [ -12022.6810] [Alpha ][ 0.301899] . ( 503 sec) [ -12022.6810] [Topology ] . ( 505 sec) [ -12022.6803] [Topology ] . ( 506 sec) [ -12022.6802] [GTR parameters ] . ( 506 sec) [ -12022.6802] [Alpha ][ 0.301899] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12027.778921 . Log likelihood obtained after SPR moves : -12022.680231 . Log likelihood of the current tree: -12022.680231. . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Best log likelihood : -12022.680231 . Time used 0h8m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1950.19user 0.00system 32:42.08elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps