.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 935 patterns found. (out of a total of 1271 sites) . 411 sites without polymorphism (32.34%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -57799.6506] [GTR parameters ] . ( 3 sec) [ -56458.4555] [Alpha ][ 0.500960] . ( 3 sec) [ -56143.2942] [13305] [depth= 8] . ( 3 sec) [ -55871.0911] [13221] [depth= 9] . ( 3 sec) [ -55835.6285] [13213] [depth= 1] . ( 4 sec) [ -55441.8988] [13181] [depth= 5] . ( 4 sec) [ -55232.1408] [13135] [depth= 3] . ( 4 sec) [ -54928.5601] [13063] [depth= 12] . ( 4 sec) [ -54893.4264] [13044] [depth= 1] . ( 4 sec) [ -54722.1022] [13023] [depth= 1] . ( 5 sec) [ -54604.6194] [12959] [depth= 3] . ( 5 sec) [ -54571.1789] [12950] [depth= 5] . ( 5 sec) [ -54269.4674] [12938] [depth= 2] . ( 5 sec) [ -54032.4916] [12931] [depth= 5] . ( 5 sec) [ -53636.6695] [12881] [depth= 10] . ( 5 sec) [ -53402.6018] [12808] [depth= 15] . ( 5 sec) [ -53398.6357] [12855] [depth= 13] . ( 5 sec) [ -53153.1791] [12818] [depth= 4] . ( 6 sec) [ -53052.8563] [12806] [depth= 6] . ( 6 sec) [ -52914.2740] [12747] [depth= 8] . ( 6 sec) [ -52446.0882] [12599] [depth= 8] . ( 6 sec) [ -51296.3979] [12589] [depth= 6] . ( 6 sec) [ -51185.4367] [12565] [depth= 8] . ( 6 sec) [ -50937.2165] [12526] [depth= 1] . ( 6 sec) [ -50931.4324] [12514] [depth= 2] . ( 7 sec) [ -50866.4920] [12509] [depth= 3] . ( 7 sec) [ -50797.4081] [12452] [depth= 7] . ( 7 sec) [ -50278.5316] [12306] [depth= 15] . ( 7 sec) [ -49928.7468] [12239] [depth= 1] . ( 7 sec) [ -49706.4028] [12145] [depth= 15] . ( 7 sec) [ -49415.6638] [12097] [depth= 3] . ( 7 sec) [ -49276.7324] [12054] [depth= 3] . ( 8 sec) [ -48836.0618] [11963] [depth= 15] . ( 8 sec) [ -48512.7375] [11881] [depth= 9] . ( 8 sec) [ -48186.4940] [11719] [depth= 8] . ( 8 sec) [ -48097.0937] [11712] [depth= 1] . ( 8 sec) [ -48074.4275] [11707] [depth= 1] . ( 8 sec) [ -48073.5623] [11715] [depth= 2] . ( 8 sec) [ -48010.1996] [11743] [depth= 1] . ( 9 sec) [ -47755.9117] [11685] [depth= 8] . ( 9 sec) [ -47667.2411] [11660] [depth= 1] . ( 9 sec) [ -47573.4359] [11611] [depth= 3] . ( 9 sec) [ -47442.8235] [11589] [depth= 1] . ( 9 sec) [ -47233.0792] [11554] [depth= 8] . ( 9 sec) [ -46617.5239] [11547] [depth= 1] . ( 9 sec) [ -44160.9431] [11537] [depth= 2] . ( 10 sec) [ -44038.1862] [11509] [depth= 1] . ( 10 sec) [ -44025.6721] [11497] [depth= 8] . ( 10 sec) [ -43923.2133] [11439] [depth= 13] . ( 10 sec) [ -43875.8130] [11390] [depth= 12] . ( 10 sec) [ -43516.1654] [11325] [depth= 10] . ( 10 sec) [ -43451.2305] [11326] [depth= 12] . ( 11 sec) [ -43283.6169] [11321] [depth= 2] . ( 11 sec) [ -42515.4376] [11305] [depth= 5] . ( 11 sec) [ -42502.7146] [11289] [depth= 1] . ( 11 sec) [ -42303.5352] [11274] [depth= 7] . ( 11 sec) [ -42256.2274] [11258] [depth= 1] . ( 11 sec) [ -42233.6762] [11237] [depth= 3] . ( 12 sec) [ -42153.3425] [11227] [depth= 1] . ( 12 sec) [ -42027.9521] [11273] [depth= 1] . ( 12 sec) [ -41822.5745] [11190] [depth= 7] . ( 12 sec) [ -41191.9494] [10987] [depth= 2] . ( 12 sec) [ -41171.8522] [10994] [depth= 9] . ( 12 sec) [ -41090.1528] [10947] [depth= 2] . ( 12 sec) [ -40980.4117] [10917] [depth= 6] . ( 13 sec) [ -40898.3068] [10909] [depth= 1] . ( 13 sec) [ -40745.1030] [10799] [depth= 8] . ( 13 sec) [ -40671.7279] [10759] [depth= 8] . ( 13 sec) [ -40514.3453] [10753] [depth= 7] . ( 13 sec) [ -40497.7970] [10749] [depth= 2] . ( 13 sec) [ -40291.6560] [10731] [depth= 8] . ( 14 sec) [ -40235.6265] [10706] [depth= 1] . ( 14 sec) [ -40172.0206] [10695] [depth= 1] . ( 14 sec) [ -40105.2450] [10677] [depth= 5] . ( 14 sec) [ -40046.5775] [10670] [depth= 1] . ( 14 sec) [ -39827.3909] [10655] [depth= 1] . ( 14 sec) [ -39821.7126] [10657] [depth= 1] . ( 15 sec) [ -39798.4336] [10645] [depth= 1] . ( 15 sec) [ -39659.0177] [10591] [depth= 4] . ( 15 sec) [ -39466.4314] [10539] [depth= 2] . ( 15 sec) [ -39368.3330] [10542] [depth= 2] . ( 15 sec) [ -39284.0400] [10500] [depth= 10] . ( 16 sec) [ -39277.5940] [10506] [depth= 1] . ( 16 sec) [ -39224.5245] [10448] [depth= 17] . ( 16 sec) [ -39208.0451] [10449] [depth= 9] . ( 16 sec) [ -39205.2362] [10453] [depth= 1] . ( 16 sec) [ -38926.6248] [10387] [depth= 2] . ( 16 sec) [ -38922.8188] [10382] [depth= 2] . ( 17 sec) [ -38910.0527] [10381] [depth= 1] . ( 17 sec) [ -38835.0757] [10383] [depth= 1] . ( 17 sec) [ -38764.3583] [10326] [depth= 17] . ( 17 sec) [ -38614.5570] [10302] [depth= 1] . ( 17 sec) [ -38604.8224] [10291] [depth= 1] . ( 17 sec) [ -38604.7223] [10291] [depth= 1] . ( 18 sec) [ -38414.2442] [10219] [depth= 1] . ( 18 sec) [ -38338.7114] [10187] [depth= 14] . ( 18 sec) [ -38232.6277] [10151] [depth= 1] . ( 18 sec) [ -38221.8932] [10141] [depth= 12] . ( 18 sec) [ -38202.9566] [10131] [depth= 1] . ( 18 sec) [ -38125.7718] [10138] [depth= 15] . ( 19 sec) [ -38051.7305] [10092] [depth= 4] . ( 19 sec) [ -37850.2824] [10012] [depth= 7] . ( 19 sec) [ -37830.2253] [ 9998] [depth= 1] . ( 19 sec) [ -37821.7630] [ 9985] [depth= 2] . ( 19 sec) [ -37740.6201] [ 9922] [depth= 2] . ( 19 sec) [ -37656.1992] [ 9884] [depth= 8] . ( 20 sec) [ -37519.8864] [ 9848] [depth= 6] . ( 20 sec) [ -37445.4234] [ 9795] [depth= 6] . ( 20 sec) [ -37188.5214] [ 9648] [depth= 12] . ( 21 sec) [ -37143.1406] [ 9631] [depth= 1] . ( 21 sec) [ -37066.6609] [ 9593] [depth= 3] . ( 21 sec) [ -37016.1852] [ 9586] [depth= 1] . ( 21 sec) [ -37010.4090] [ 9571] [depth= 3] . ( 21 sec) [ -37007.3004] [ 9574] [depth= 1] . ( 21 sec) [ -36981.9851] [ 9572] [depth= 1] . ( 21 sec) [ -36965.4080] [ 9570] [depth= 3] . ( 22 sec) [ -36911.0300] [ 9542] [depth= 8] . ( 22 sec) [ -36892.8153] [ 9530] [depth= 1] . ( 22 sec) [ -36860.1209] [ 9518] [depth= 1] . ( 22 sec) [ -36851.2864] [ 9504] [depth= 3] . ( 22 sec) [ -36822.3936] [ 9496] [depth= 1] . ( 22 sec) [ -36793.0642] [ 9488] [depth= 1] . ( 23 sec) [ -36785.7679] [ 9480] [depth= 1] . ( 23 sec) [ -36784.5543] [ 9484] [depth= 1] . ( 23 sec) [ -36768.7518] [ 9480] [depth= 1] . ( 23 sec) [ -36680.8093] [ 9458] [depth= 3] . ( 23 sec) [ -36572.7823] [ 9438] [depth= 2] . ( 24 sec) [ -36571.6420] [ 9443] [depth= 1] . ( 24 sec) [ -36558.0519] [ 9435] [depth= 2] . ( 24 sec) [ -36543.1278] [ 9445] [depth= 1] . ( 24 sec) [ -36488.3420] [ 9397] [depth= 8] . ( 25 sec) [ -35906.3615] [Branch lengths ] . ( 29 sec) [ -35726.1571] [GTR parameters ] . ( 29 sec) [ -35712.4868] [Alpha ][ 0.431066] . ( 29 sec) [ -35710.8562] [ 9393] [depth= 1] . ( 29 sec) [ -35687.6173] [ 9371] [depth= 7] . ( 30 sec) [ -35686.9647] [ 9368] [depth= 1] . ( 30 sec) [ -35686.4767] [ 9359] [depth= 1] . ( 30 sec) [ -35650.7844] [ 9349] [depth= 5] . ( 31 sec) [ -35634.3105] [ 9337] [depth= 2] . ( 31 sec) [ -35620.2640] [ 9329] [depth= 2] . ( 32 sec) [ -35608.4165] [ 9324] [depth= 1] . ( 32 sec) [ -35606.3061] [ 9325] [depth= 1] . ( 32 sec) [ -35606.2423] [ 9324] [depth= 1] . ( 33 sec) [ -35593.3880] [ 9335] [depth= 1] . ( 33 sec) [ -35514.9920] [ 9338] [depth= 1] . ( 34 sec) [ -35500.2721] [ 9328] [depth= 2] . ( 35 sec) [ -35459.4678] [ 9319] [depth= 3] . ( 35 sec) [ -35448.0973] [ 9326] [depth= 1] . ( 35 sec) [ -35445.1759] [ 9325] [depth= 2] . ( 36 sec) [ -35438.8806] [ 9319] [depth= 1] . ( 36 sec) [ -35429.7777] [ 9319] [depth= 1] . ( 36 sec) [ -35414.0671] [ 9318] [depth= 1] . ( 37 sec) [ -35409.7712] [ 9312] [depth= 1] . ( 37 sec) [ -35407.6738] [ 9309] [depth= 1] . ( 38 sec) [ -35401.8042] [ 9300] [depth= 2] . ( 40 sec) [ -35397.2856] [ 9300] [depth= 1] . ( 41 sec) [ -35395.4835] [ 9290] [depth= 1] . ( 41 sec) [ -35395.1085] [ 9296] [depth= 1] . ( 42 sec) [ -35389.0575] [ 9291] [depth= 1] . ( 42 sec) [ -35381.1055] [ 9290] [depth= 1] . ( 43 sec) [ -35335.6873] [ 9288] [depth= 9] . ( 44 sec) [ -35237.9970] [Branch lengths ] . ( 46 sec) [ -35233.1272] [GTR parameters ] . ( 47 sec) [ -35231.8460] [Alpha ][ 0.450784] . ( 50 sec) [ -35230.8193] [ 9289] [depth= 3] . ( 52 sec) [ -35230.4099] [ 9295] [depth= 2] . ( 53 sec) [ -35229.1963] [ 9299] [depth= 1] . ( 56 sec) [ -35223.6470] [ 9296] [depth= 3] . ( 56 sec) [ -35221.6868] [ 9300] [depth= 1] . ( 57 sec) [ -35220.6967] [ 9298] [depth= 2] . ( 57 sec) [ -35220.6740] [ 9296] [depth= 1] . ( 58 sec) [ -35220.5887] [ 9295] [depth= 1] . ( 58 sec) [ -35220.4724] [ 9294] [depth= 1] . ( 59 sec) [ -35219.3902] [ 9298] [depth= 1] . ( 60 sec) [ -35218.0769] [ 9301] [depth= 1] . ( 61 sec) [ -35215.4260] [ 9299] [depth= 1] . ( 62 sec) [ -35186.7157] [Branch lengths ] . ( 64 sec) [ -35185.3356] [GTR parameters ] . ( 65 sec) [ -35185.2216] [Alpha ][ 0.456702] . ( 68 sec) [ -35184.2064] [ 9299] [depth= 2] . ( 70 sec) [ -35183.3341] [ 9295] [depth= 2] . ( 71 sec) [ -35180.7929] [ 9292] [depth= 1] . ( 81 sec) [ -35160.6202] [Branch lengths ] . ( 83 sec) [ -35159.0432] [GTR parameters ] . ( 83 sec) [ -35159.0421] [Alpha ][ 0.456117] . ( 85 sec) [ -35158.8845] [ 9295] [depth= 1] . ( 86 sec) [ -35158.3003] [ 9300] [depth= 2] . ( 91 sec) [ -35156.0859] [ 9302] [depth= 1] . ( 100 sec) [ -35155.9893] [ 9303] [depth= 1] . ( 101 sec) [ -35135.5518] [Branch lengths ] . ( 103 sec) [ -35134.3057] [GTR parameters ] . ( 103 sec) [ -35134.2407] [Alpha ][ 0.451896] . ( 119 sec) [ -35123.9829] [Branch lengths ] . ( 191 sec) [ -35123.6815] [ 9312] [depth= 3] . ( 207 sec) [ -35118.5567] [Branch lengths ] . ( 209 sec) [ -35117.1876] [GTR parameters ] . ( 209 sec) [ -35116.7840] [Alpha ][ 0.441847] . ( 300 sec) [ -35113.6576] [Branch lengths ] . ( 300 sec) [ -35113.6576] [Topology ] . ( 303 sec) [ -35112.7874] [Topology ] . ( 305 sec) [ -35112.3357] [Topology ] . ( 307 sec) [ -35112.0223] [Topology ] . ( 310 sec) [ -35111.7949] [Topology ] . ( 312 sec) [ -35111.6275] [Topology ] . ( 314 sec) [ -35111.3520] [Topology ] . ( 317 sec) [ -35110.7559] [Topology ] . ( 319 sec) [ -35110.5203] [Topology ] . ( 321 sec) [ -35110.3717] [Topology ] . ( 325 sec) [ -35108.9771] [GTR parameters ] . ( 326 sec) [ -35108.4344] [Alpha ][ 0.430913] . ( 326 sec) [ -35108.4344] [Topology ] . ( 328 sec) [ -35107.9467] [Topology ] . ( 330 sec) [ -35107.6407] [Topology ] . ( 332 sec) [ -35107.4248] [Topology ] . ( 335 sec) [ -35107.2707] [Topology ] . ( 337 sec) [ -35107.1602] [Topology ] . ( 339 sec) [ -35107.0810] [Topology ] . ( 341 sec) [ -35106.8812] [GTR parameters ] . ( 341 sec) [ -35106.7649] [Alpha ][ 0.425989] . ( 342 sec) [ -35106.7649] [Topology ] . ( 344 sec) [ -35106.5993] [Topology ] . ( 346 sec) [ -35106.4908] [Topology ] . ( 348 sec) [ -35106.4142] [Topology ] . ( 351 sec) [ -35106.3601] [Topology ] . ( 353 sec) [ -35106.3216] [Topology ] . ( 355 sec) [ -35106.2944] [Topology ] . ( 357 sec) [ -35106.2386] [GTR parameters ] . ( 358 sec) [ -35106.1968] [Alpha ][ 0.423082] . ( 358 sec) [ -35106.1968] [Topology ] . ( 360 sec) [ -35106.1423] [Topology ] . ( 362 sec) [ -35106.1066] [Topology ] . ( 365 sec) [ -35106.0817] [Topology ] . ( 367 sec) [ -35106.0642] [Topology ] . ( 369 sec) [ -35106.0518] [Topology ] . ( 371 sec) [ -35106.0431] [Topology ] . ( 373 sec) [ -35106.0257] [GTR parameters ] . ( 373 sec) [ -35106.0113] [Alpha ][ 0.421392] . ( 373 sec) [ -35106.0113] [Topology ] . ( 375 sec) [ -35105.9937] [Topology ] . ( 377 sec) [ -35105.9822] [Topology ] . ( 380 sec) [ -35105.9742] [Topology ] . ( 382 sec) [ -35105.9686] [Topology ] . ( 384 sec) [ -35105.9647] [Topology ] . ( 387 sec) [ -35105.9619] [Topology ] . ( 388 sec) [ -35105.9568] [GTR parameters ] . ( 388 sec) [ -35105.9522] [Alpha ][ 0.420434] . ( 388 sec) [ -35105.9522] [Topology ] . ( 390 sec) [ -35105.9467] [Topology ] . ( 393 sec) [ -35105.9432] [Topology ] . ( 395 sec) [ -35105.9407] [Topology ] . ( 397 sec) [ -35105.9390] [Topology ] . ( 400 sec) [ -35105.9378] [Topology ] . ( 402 sec) [ -35105.9370] [Topology ] . ( 402 sec) [ -35105.9354] [GTR parameters ] . ( 403 sec) [ -35105.9339] [Alpha ][ 0.419886] . ( 403 sec) [ -35105.9339] [Topology ] . ( 405 sec) [ -35105.9322] [Topology ] . ( 407 sec) [ -35105.9311] [Topology ] . ( 410 sec) [ -35105.9304] [Topology ] . ( 410 sec) [ -35105.9301] [GTR parameters ] . ( 410 sec) [ -35105.9301] [Alpha ][ 0.419886] . ( 410 sec) [ -35105.9301] [Topology ] . ( 413 sec) [ -35105.9294] [Topology ] . ( 413 sec) [ -35105.9294] [GTR parameters ] . ( 414 sec) [ -35105.9292] [Alpha ][ 0.419466] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35105.929195. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 8 sec) [ -56598.1561] [GTR parameters ] . ( 8 sec) [ -55334.2815] [Alpha ][ 0.500960] . ( 8 sec) [ -54909.0182] [13289] [depth= 11] . ( 8 sec) [ -54418.2238] [13180] [depth= 12] . ( 9 sec) [ -54383.1279] [13159] [depth= 1] . ( 9 sec) [ -54135.5955] [13085] [depth= 9] . ( 9 sec) [ -54015.7245] [13029] [depth= 1] . ( 9 sec) [ -53648.3221] [12968] [depth= 7] . ( 9 sec) [ -53570.0010] [12953] [depth= 1] . ( 9 sec) [ -53070.7714] [12945] [depth= 6] . ( 9 sec) [ -53063.1792] [12930] [depth= 4] . ( 10 sec) [ -52902.0083] [12883] [depth= 3] . ( 10 sec) [ -52859.7482] [12881] [depth= 2] . ( 10 sec) [ -52785.6896] [12861] [depth= 4] . ( 10 sec) [ -52400.9421] [12826] [depth= 3] . ( 10 sec) [ -52081.2296] [12781] [depth= 1] . ( 10 sec) [ -52050.6774] [12766] [depth= 3] . ( 10 sec) [ -51756.6997] [12740] [depth= 4] . ( 10 sec) [ -50140.3346] [12672] [depth= 13] . ( 11 sec) [ -49377.7491] [12658] [depth= 8] . ( 11 sec) [ -49091.6240] [12648] [depth= 7] . ( 11 sec) [ -48906.2602] [12649] [depth= 2] . ( 11 sec) [ -48698.7386] [12611] [depth= 1] . ( 11 sec) [ -48178.6346] [12536] [depth= 4] . ( 11 sec) [ -47977.1504] [12473] [depth= 12] . ( 12 sec) [ -47264.3927] [12440] [depth= 2] . ( 12 sec) [ -47149.3992] [12364] [depth= 4] . ( 12 sec) [ -47025.0876] [12358] [depth= 1] . ( 12 sec) [ -46677.0771] [12221] [depth= 10] . ( 12 sec) [ -46310.3693] [12070] [depth= 25] . ( 12 sec) [ -46136.1917] [12027] [depth= 13] . ( 12 sec) [ -45972.7932] [12020] [depth= 11] . ( 13 sec) [ -45219.9296] [11821] [depth= 9] . ( 13 sec) [ -45188.8716] [11804] [depth= 2] . ( 13 sec) [ -45001.4537] [11747] [depth= 12] . ( 13 sec) [ -44875.6237] [11704] [depth= 3] . ( 13 sec) [ -44768.8885] [11692] [depth= 8] . ( 13 sec) [ -44749.0235] [11687] [depth= 1] . ( 13 sec) [ -44571.6932] [11601] [depth= 15] . ( 14 sec) [ -44487.6791] [11570] [depth= 5] . ( 14 sec) [ -44354.2444] [11605] [depth= 1] . ( 14 sec) [ -44238.3300] [11539] [depth= 20] . ( 14 sec) [ -44123.0500] [11521] [depth= 2] . ( 14 sec) [ -43941.1792] [11444] [depth= 1] . ( 14 sec) [ -43859.7997] [11440] [depth= 2] . ( 15 sec) [ -43702.3722] [11380] [depth= 5] . ( 15 sec) [ -43589.5241] [11346] [depth= 11] . ( 15 sec) [ -43428.9594] [11293] [depth= 9] . ( 15 sec) [ -43416.5559] [11325] [depth= 3] . ( 15 sec) [ -43201.5980] [11243] [depth= 5] . ( 15 sec) [ -43100.3222] [11179] [depth= 1] . ( 15 sec) [ -42956.1094] [11121] [depth= 6] . ( 16 sec) [ -42877.6308] [11090] [depth= 11] . ( 16 sec) [ -42816.5273] [11047] [depth= 17] . ( 16 sec) [ -42770.7384] [11037] [depth= 3] . ( 16 sec) [ -42688.6615] [11030] [depth= 2] . ( 16 sec) [ -42570.7035] [11001] [depth= 1] . ( 16 sec) [ -42345.2893] [10908] [depth= 16] . ( 17 sec) [ -41980.7638] [10956] [depth= 11] . ( 17 sec) [ -41887.4458] [10943] [depth= 1] . ( 17 sec) [ -41857.3732] [10915] [depth= 2] . ( 17 sec) [ -41834.0598] [10903] [depth= 2] . ( 17 sec) [ -41660.6122] [10866] [depth= 7] . ( 18 sec) [ -41584.9118] [10847] [depth= 11] . ( 18 sec) [ -41090.7173] [10810] [depth= 11] . ( 18 sec) [ -40834.2681] [10713] [depth= 4] . ( 18 sec) [ -40755.1930] [10694] [depth= 4] . ( 18 sec) [ -40736.9748] [10667] [depth= 5] . ( 19 sec) [ -40731.1246] [10668] [depth= 1] . ( 19 sec) [ -40577.7950] [10601] [depth= 5] . ( 19 sec) [ -40559.2876] [10584] [depth= 1] . ( 19 sec) [ -40538.8148] [10577] [depth= 1] . ( 19 sec) [ -40530.1985] [10538] [depth= 7] . ( 20 sec) [ -40500.2125] [10527] [depth= 3] . ( 20 sec) [ -40402.1924] [10485] [depth= 5] . ( 20 sec) [ -40386.6823] [10483] [depth= 1] . ( 20 sec) [ -40102.9208] [10440] [depth= 9] . ( 20 sec) [ -39984.0976] [10464] [depth= 1] . ( 20 sec) [ -39961.8396] [10440] [depth= 1] . ( 20 sec) [ -39940.3045] [10442] [depth= 8] . ( 21 sec) [ -39781.2317] [10393] [depth= 4] . ( 21 sec) [ -39778.5352] [10396] [depth= 1] . ( 21 sec) [ -39681.7579] [10390] [depth= 1] . ( 21 sec) [ -39497.3287] [10349] [depth= 4] . ( 21 sec) [ -39480.5320] [10352] [depth= 1] . ( 21 sec) [ -39386.8194] [10315] [depth= 1] . ( 22 sec) [ -39266.4351] [10241] [depth= 7] . ( 22 sec) [ -39256.9102] [10248] [depth= 1] . ( 22 sec) [ -39128.6021] [10178] [depth= 11] . ( 22 sec) [ -39104.3484] [10172] [depth= 1] . ( 22 sec) [ -39057.3187] [10157] [depth= 1] . ( 22 sec) [ -38881.3114] [10117] [depth= 5] . ( 22 sec) [ -38754.6962] [10085] [depth= 12] . ( 23 sec) [ -38634.5031] [10055] [depth= 10] . ( 23 sec) [ -38615.8669] [10039] [depth= 7] . ( 23 sec) [ -38559.0024] [10059] [depth= 1] . ( 23 sec) [ -38516.4825] [10046] [depth= 4] . ( 23 sec) [ -38355.6526] [10015] [depth= 5] . ( 24 sec) [ -38308.4303] [10020] [depth= 7] . ( 24 sec) [ -38248.6951] [ 9993] [depth= 1] . ( 24 sec) [ -38179.8737] [ 9972] [depth= 1] . ( 24 sec) [ -38057.3319] [ 9967] [depth= 1] . ( 24 sec) [ -38042.7896] [ 9953] [depth= 8] . ( 25 sec) [ -37969.8318] [ 9923] [depth= 4] . ( 25 sec) [ -37952.8089] [ 9914] [depth= 1] . ( 25 sec) [ -37924.7591] [ 9914] [depth= 2] . ( 25 sec) [ -37857.6674] [ 9881] [depth= 4] . ( 25 sec) [ -37641.3754] [ 9800] [depth= 7] . ( 26 sec) [ -37623.2029] [ 9786] [depth= 1] . ( 26 sec) [ -37592.8669] [ 9814] [depth= 1] . ( 26 sec) [ -37580.4758] [ 9786] [depth= 1] . ( 26 sec) [ -37385.4217] [ 9689] [depth= 11] . ( 26 sec) [ -37304.5124] [ 9653] [depth= 3] . ( 26 sec) [ -37270.3402] [ 9631] [depth= 4] . ( 27 sec) [ -37169.1445] [ 9588] [depth= 2] . ( 27 sec) [ -37149.9551] [ 9595] [depth= 1] . ( 27 sec) [ -37028.0105] [ 9604] [depth= 2] . ( 27 sec) [ -36884.8363] [ 9576] [depth= 1] . ( 27 sec) [ -36864.9982] [ 9569] [depth= 1] . ( 27 sec) [ -36858.3193] [ 9560] [depth= 2] . ( 28 sec) [ -36852.6564] [ 9565] [depth= 1] . ( 28 sec) [ -36810.6518] [ 9562] [depth= 2] . ( 28 sec) [ -36804.2902] [ 9562] [depth= 1] . ( 28 sec) [ -36796.2119] [ 9558] [depth= 1] . ( 28 sec) [ -36793.0843] [ 9571] [depth= 1] . ( 29 sec) [ -36788.7239] [ 9576] [depth= 1] . ( 29 sec) [ -36765.2364] [ 9543] [depth= 6] . ( 29 sec) [ -36761.5012] [ 9539] [depth= 1] . ( 29 sec) [ -36726.7979] [ 9546] [depth= 3] . ( 30 sec) [ -36183.5857] [Branch lengths ] . ( 34 sec) [ -36006.0747] [GTR parameters ] . ( 34 sec) [ -35999.3182] [Alpha ][ 0.451076] . ( 34 sec) [ -35998.6594] [ 9548] [depth= 1] . ( 35 sec) [ -35975.9394] [ 9533] [depth= 2] . ( 35 sec) [ -35975.1600] [ 9537] [depth= 1] . ( 35 sec) [ -35964.8224] [ 9531] [depth= 1] . ( 35 sec) [ -35952.7846] [ 9519] [depth= 1] . ( 36 sec) [ -35880.5659] [ 9474] [depth= 4] . ( 36 sec) [ -35877.4891] [ 9465] [depth= 1] . ( 36 sec) [ -35845.7023] [ 9450] [depth= 1] . ( 36 sec) [ -35826.4215] [ 9474] [depth= 10] . ( 37 sec) [ -35825.3456] [ 9478] [depth= 1] . ( 37 sec) [ -35717.1766] [ 9438] [depth= 2] . ( 37 sec) [ -35714.7710] [ 9435] [depth= 1] . ( 37 sec) [ -35672.4200] [ 9426] [depth= 1] . ( 37 sec) [ -35653.1127] [ 9417] [depth= 1] . ( 37 sec) [ -35651.3007] [ 9417] [depth= 1] . ( 38 sec) [ -35639.2568] [ 9412] [depth= 1] . ( 38 sec) [ -35562.9810] [ 9389] [depth= 3] . ( 39 sec) [ -35561.4064] [ 9384] [depth= 1] . ( 39 sec) [ -35559.1259] [ 9387] [depth= 1] . ( 39 sec) [ -35556.0966] [ 9384] [depth= 1] . ( 39 sec) [ -35475.9206] [ 9366] [depth= 6] . ( 39 sec) [ -35460.0375] [ 9348] [depth= 2] . ( 40 sec) [ -35429.2784] [ 9344] [depth= 2] . ( 40 sec) [ -35418.8947] [ 9350] [depth= 1] . ( 40 sec) [ -35413.0083] [ 9328] [depth= 3] . ( 41 sec) [ -35410.6707] [ 9328] [depth= 1] . ( 41 sec) [ -35401.0669] [ 9317] [depth= 1] . ( 41 sec) [ -35400.0893] [ 9318] [depth= 1] . ( 42 sec) [ -35399.6187] [ 9314] [depth= 4] . ( 42 sec) [ -35393.7867] [ 9309] [depth= 3] . ( 43 sec) [ -35391.6806] [ 9300] [depth= 1] . ( 44 sec) [ -35375.3865] [ 9284] [depth= 1] . ( 44 sec) [ -35371.8088] [ 9282] [depth= 1] . ( 44 sec) [ -35369.8763] [ 9279] [depth= 1] . ( 45 sec) [ -35368.8807] [ 9284] [depth= 2] . ( 45 sec) [ -35366.2053] [ 9286] [depth= 1] . ( 45 sec) [ -35356.6223] [ 9291] [depth= 1] . ( 45 sec) [ -35343.7769] [ 9293] [depth= 5] . ( 48 sec) [ -35342.8533] [ 9298] [depth= 1] . ( 50 sec) [ -35239.8428] [Branch lengths ] . ( 53 sec) [ -35231.7357] [GTR parameters ] . ( 53 sec) [ -35231.6824] [Alpha ][ 0.455256] . ( 55 sec) [ -35231.2564] [ 9299] [depth= 1] . ( 58 sec) [ -35230.0860] [ 9294] [depth= 1] . ( 64 sec) [ -35227.9902] [ 9289] [depth= 1] . ( 70 sec) [ -35201.9209] [Branch lengths ] . ( 72 sec) [ -35199.9141] [GTR parameters ] . ( 73 sec) [ -35199.8907] [Alpha ][ 0.457933] . ( 75 sec) [ -35199.7957] [ 9287] [depth= 3] . ( 89 sec) [ -35183.2358] [Branch lengths ] . ( 90 sec) [ -35181.9735] [GTR parameters ] . ( 90 sec) [ -35181.9696] [Alpha ][ 0.456842] . ( 106 sec) [ -35170.8715] [Branch lengths ] . ( 138 sec) [ -35169.2359] [ 9310] [depth= 2] . ( 139 sec) [ -35159.6826] [ 9315] [depth= 1] . ( 142 sec) [ -35158.5053] [ 9312] [depth= 1] . ( 149 sec) [ -35158.0540] [ 9316] [depth= 1] . ( 157 sec) [ -35157.4905] [ 9324] [depth= 2] . ( 163 sec) [ -35155.4335] [ 9320] [depth= 1] . ( 164 sec) [ -35154.8157] [ 9324] [depth= 1] . ( 167 sec) [ -35153.5976] [ 9320] [depth= 1] . ( 172 sec) [ -35153.5595] [ 9323] [depth= 1] . ( 181 sec) [ -35153.5010] [ 9328] [depth= 1] . ( 190 sec) [ -35136.8335] [Branch lengths ] . ( 193 sec) [ -35135.1292] [GTR parameters ] . ( 193 sec) [ -35134.7919] [Alpha ][ 0.447507] . ( 212 sec) [ -35134.6475] [ 9332] [depth= 1] . ( 238 sec) [ -35133.3620] [ 9332] [depth= 2] . ( 262 sec) [ -35130.6203] [ 9315] [depth= 2] . ( 274 sec) [ -35130.0677] [ 9315] [depth= 1] . ( 274 sec) [ -35127.9371] [ 9318] [depth= 1] . ( 277 sec) [ -35127.1717] [ 9312] [depth= 1] . ( 281 sec) [ -35118.5253] [Branch lengths ] . ( 283 sec) [ -35118.1030] [GTR parameters ] . ( 283 sec) [ -35117.9843] [Alpha ][ 0.442043] . ( 372 sec) [ -35114.3681] [Branch lengths ] . ( 372 sec) [ -35114.3681] [Topology ] . ( 375 sec) [ -35113.3187] [Topology ] . ( 377 sec) [ -35112.7699] [Topology ] . ( 379 sec) [ -35112.3865] [Topology ] . ( 382 sec) [ -35112.1075] [Topology ] . ( 384 sec) [ -35111.9021] [Topology ] . ( 386 sec) [ -35111.7500] [Topology ] . ( 389 sec) [ -35110.8876] [GTR parameters ] . ( 389 sec) [ -35110.6032] [Alpha ][ 0.433973] . ( 389 sec) [ -35110.6032] [Topology ] . ( 391 sec) [ -35109.8899] [Topology ] . ( 394 sec) [ -35108.9924] [Topology ] . ( 396 sec) [ -35108.5408] [Topology ] . ( 398 sec) [ -35108.2375] [Topology ] . ( 400 sec) [ -35108.0233] [Topology ] . ( 403 sec) [ -35107.8703] [Topology ] . ( 405 sec) [ -35107.7603] [Topology ] . ( 408 sec) [ -35107.4183] [GTR parameters ] . ( 408 sec) [ -35107.2265] [Alpha ][ 0.427593] . ( 408 sec) [ -35107.2265] [Topology ] . ( 410 sec) [ -35106.9746] [Topology ] . ( 413 sec) [ -35106.8077] [Topology ] . ( 415 sec) [ -35106.6893] [Topology ] . ( 417 sec) [ -35106.6049] [Topology ] . ( 420 sec) [ -35106.5448] [Topology ] . ( 422 sec) [ -35106.5021] [Topology ] . ( 424 sec) [ -35106.4130] [GTR parameters ] . ( 424 sec) [ -35106.3510] [Alpha ][ 0.424033] . ( 424 sec) [ -35106.3510] [Topology ] . ( 426 sec) [ -35106.2660] [Topology ] . ( 429 sec) [ -35106.2103] [Topology ] . ( 431 sec) [ -35106.1712] [Topology ] . ( 433 sec) [ -35106.1436] [Topology ] . ( 436 sec) [ -35106.1241] [Topology ] . ( 438 sec) [ -35106.1103] [Topology ] . ( 439 sec) [ -35106.0831] [GTR parameters ] . ( 440 sec) [ -35106.0612] [Alpha ][ 0.421939] . ( 440 sec) [ -35106.0612] [Topology ] . ( 442 sec) [ -35106.0333] [Topology ] . ( 444 sec) [ -35106.0152] [Topology ] . ( 447 sec) [ -35106.0026] [Topology ] . ( 449 sec) [ -35105.9937] [Topology ] . ( 451 sec) [ -35105.9875] [Topology ] . ( 453 sec) [ -35105.9831] [Topology ] . ( 455 sec) [ -35105.9753] [GTR parameters ] . ( 455 sec) [ -35105.9678] [Alpha ][ 0.420722] . ( 455 sec) [ -35105.9678] [Topology ] . ( 458 sec) [ -35105.9592] [Topology ] . ( 460 sec) [ -35105.9536] [Topology ] . ( 462 sec) [ -35105.9497] [Topology ] . ( 464 sec) [ -35105.9470] [Topology ] . ( 467 sec) [ -35105.9451] [Topology ] . ( 469 sec) [ -35105.9438] [Topology ] . ( 470 sec) [ -35105.9411] [GTR parameters ] . ( 471 sec) [ -35105.9389] [Alpha ][ 0.420048] . ( 471 sec) [ -35105.9389] [Topology ] . ( 473 sec) [ -35105.9361] [Topology ] . ( 475 sec) [ -35105.9343] [Topology ] . ( 478 sec) [ -35105.9331] [Topology ] . ( 480 sec) [ -35105.9322] [Topology ] . ( 481 sec) [ -35105.9317] [GTR parameters ] . ( 481 sec) [ -35105.9314] [Alpha ][ 0.419628] . ( 481 sec) [ -35105.9314] [Topology ] . ( 483 sec) [ -35105.9301] [Topology ] . ( 486 sec) [ -35105.9293] [Topology ] . ( 486 sec) [ -35105.9292] [GTR parameters ] . ( 486 sec) [ -35105.9292] [Alpha ][ 0.419628] . ( 486 sec) [ -35105.9292] [Topology ] . ( 489 sec) [ -35105.9286] [Topology ] . ( 489 sec) [ -35105.9285] [GTR parameters ] . ( 489 sec) [ -35105.9285] [Alpha ][ 0.419628] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35105.928538. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -55555.5740] [GTR parameters ] . ( 3 sec) [ -54287.8475] [Alpha ][ 0.500960] . ( 3 sec) [ -53592.0272] [13086] [depth= 7] . ( 4 sec) [ -53110.4925] [12982] [depth= 10] . ( 4 sec) [ -52430.2411] [12847] [depth= 7] . ( 4 sec) [ -52405.2519] [12840] [depth= 1] . ( 4 sec) [ -51634.7353] [12705] [depth= 7] . ( 4 sec) [ -51589.2114] [12687] [depth= 4] . ( 4 sec) [ -51373.2289] [12646] [depth= 1] . ( 4 sec) [ -51080.8782] [12473] [depth= 5] . ( 4 sec) [ -50990.5762] [12451] [depth= 3] . ( 5 sec) [ -50865.1758] [12436] [depth= 3] . ( 5 sec) [ -50852.3133] [12430] [depth= 3] . ( 5 sec) [ -50625.6970] [12425] [depth= 3] . ( 5 sec) [ -50580.5587] [12429] [depth= 5] . ( 5 sec) [ -50553.0435] [12413] [depth= 10] . ( 5 sec) [ -50392.3376] [12391] [depth= 2] . ( 5 sec) [ -50346.5827] [12360] [depth= 3] . ( 6 sec) [ -50296.7833] [12337] [depth= 2] . ( 6 sec) [ -50199.3687] [12304] [depth= 8] . ( 6 sec) [ -49988.5136] [12276] [depth= 1] . ( 6 sec) [ -49886.3177] [12190] [depth= 9] . ( 6 sec) [ -49841.8086] [12184] [depth= 1] . ( 6 sec) [ -49729.6002] [12169] [depth= 1] . ( 6 sec) [ -49710.8125] [12151] [depth= 12] . ( 7 sec) [ -49632.5048] [12118] [depth= 10] . ( 7 sec) [ -49444.7226] [12103] [depth= 3] . ( 7 sec) [ -49400.3625] [12064] [depth= 10] . ( 7 sec) [ -49258.6880] [12003] [depth= 11] . ( 7 sec) [ -49007.0394] [11980] [depth= 1] . ( 7 sec) [ -48700.9333] [11872] [depth= 14] . ( 8 sec) [ -48487.2176] [11804] [depth= 1] . ( 8 sec) [ -48286.6853] [11723] [depth= 11] . ( 8 sec) [ -48178.7552] [11690] [depth= 1] . ( 8 sec) [ -48071.8567] [11635] [depth= 9] . ( 8 sec) [ -48021.4154] [11631] [depth= 1] . ( 8 sec) [ -47899.7393] [11571] [depth= 2] . ( 9 sec) [ -47834.6907] [11572] [depth= 1] . ( 9 sec) [ -47715.4022] [11547] [depth= 11] . ( 9 sec) [ -47647.2784] [11549] [depth= 1] . ( 9 sec) [ -47533.3760] [11538] [depth= 4] . ( 9 sec) [ -47436.8871] [11500] [depth= 8] . ( 9 sec) [ -47431.4728] [11556] [depth= 1] . ( 10 sec) [ -47369.6551] [11556] [depth= 1] . ( 10 sec) [ -47354.1271] [11544] [depth= 7] . ( 10 sec) [ -47342.7770] [11547] [depth= 1] . ( 10 sec) [ -47317.3294] [11529] [depth= 6] . ( 10 sec) [ -45461.9385] [11498] [depth= 7] . ( 10 sec) [ -45417.3197] [11478] [depth= 5] . ( 10 sec) [ -44993.9038] [11414] [depth= 2] . ( 11 sec) [ -44839.3870] [11348] [depth= 1] . ( 11 sec) [ -44722.9968] [11334] [depth= 7] . ( 11 sec) [ -44496.3879] [11246] [depth= 11] . ( 11 sec) [ -44393.1077] [11222] [depth= 2] . ( 11 sec) [ -44272.6637] [11238] [depth= 10] . ( 11 sec) [ -44011.5998] [11168] [depth= 2] . ( 12 sec) [ -43975.0460] [11152] [depth= 1] . ( 12 sec) [ -43844.6459] [11128] [depth= 7] . ( 12 sec) [ -43688.8323] [11064] [depth= 10] . ( 12 sec) [ -43527.7103] [11020] [depth= 13] . ( 12 sec) [ -43500.3147] [11009] [depth= 1] . ( 13 sec) [ -43423.7482] [10985] [depth= 6] . ( 13 sec) [ -43115.8324] [10963] [depth= 1] . ( 13 sec) [ -42933.1092] [10881] [depth= 10] . ( 13 sec) [ -42912.3676] [10918] [depth= 1] . ( 13 sec) [ -42670.9589] [10826] [depth= 18] . ( 13 sec) [ -42292.4746] [10864] [depth= 15] . ( 14 sec) [ -42184.3849] [10794] [depth= 1] . ( 14 sec) [ -42147.7664] [10788] [depth= 8] . ( 14 sec) [ -42121.8357] [10792] [depth= 1] . ( 14 sec) [ -42079.1202] [10768] [depth= 1] . ( 14 sec) [ -42016.2150] [10749] [depth= 8] . ( 14 sec) [ -41835.2231] [10683] [depth= 11] . ( 15 sec) [ -41829.0895] [10730] [depth= 1] . ( 15 sec) [ -41695.5854] [10571] [depth= 15] . ( 15 sec) [ -41668.6311] [10596] [depth= 14] . ( 15 sec) [ -41660.8906] [10571] [depth= 3] . ( 15 sec) [ -41600.2207] [10568] [depth= 1] . ( 15 sec) [ -41578.3606] [10542] [depth= 5] . ( 15 sec) [ -41426.4839] [10475] [depth= 6] . ( 16 sec) [ -41414.6326] [10461] [depth= 3] . ( 16 sec) [ -41329.8562] [10417] [depth= 7] . ( 16 sec) [ -40588.0552] [10394] [depth= 6] . ( 16 sec) [ -40291.3144] [10383] [depth= 1] . ( 16 sec) [ -40072.5759] [10348] [depth= 7] . ( 17 sec) [ -40021.5281] [10324] [depth= 9] . ( 17 sec) [ -39697.0971] [10294] [depth= 6] . ( 17 sec) [ -39534.4129] [10244] [depth= 12] . ( 17 sec) [ -39490.4702] [10215] [depth= 2] . ( 17 sec) [ -39380.4274] [10163] [depth= 1] . ( 17 sec) [ -39270.7836] [10117] [depth= 3] . ( 18 sec) [ -38985.2031] [10099] [depth= 3] . ( 18 sec) [ -38974.4706] [10094] [depth= 2] . ( 18 sec) [ -38916.2634] [10078] [depth= 2] . ( 18 sec) [ -38838.2633] [10025] [depth= 6] . ( 18 sec) [ -38519.3436] [ 9954] [depth= 3] . ( 19 sec) [ -38461.0651] [ 9906] [depth= 1] . ( 19 sec) [ -38449.7294] [ 9868] [depth= 1] . ( 19 sec) [ -38080.8561] [ 9740] [depth= 3] . ( 19 sec) [ -37966.4181] [ 9710] [depth= 1] . ( 19 sec) [ -37811.0816] [ 9695] [depth= 1] . ( 20 sec) [ -37791.9167] [ 9684] [depth= 1] . ( 20 sec) [ -37786.8785] [ 9668] [depth= 1] . ( 20 sec) [ -37728.0117] [ 9651] [depth= 1] . ( 20 sec) [ -37578.5525] [ 9624] [depth= 2] . ( 20 sec) [ -37564.3763] [ 9610] [depth= 3] . ( 21 sec) [ -37445.7213] [ 9559] [depth= 1] . ( 21 sec) [ -37414.4823] [ 9542] [depth= 2] . ( 21 sec) [ -37374.1616] [ 9536] [depth= 2] . ( 21 sec) [ -37344.2454] [ 9523] [depth= 2] . ( 21 sec) [ -37199.1159] [ 9525] [depth= 2] . ( 21 sec) [ -37172.4947] [ 9540] [depth= 10] . ( 22 sec) [ -37157.1230] [ 9528] [depth= 1] . ( 22 sec) [ -37156.2209] [ 9529] [depth= 1] . ( 22 sec) [ -37136.3692] [ 9529] [depth= 1] . ( 22 sec) [ -37056.7364] [ 9520] [depth= 3] . ( 22 sec) [ -36863.0263] [ 9538] [depth= 1] . ( 22 sec) [ -36807.8106] [ 9520] [depth= 1] . ( 22 sec) [ -36764.9208] [ 9501] [depth= 5] . ( 23 sec) [ -36752.2206] [ 9499] [depth= 1] . ( 23 sec) [ -36749.2705] [ 9502] [depth= 1] . ( 23 sec) [ -36738.0916] [ 9512] [depth= 4] . ( 23 sec) [ -36732.9433] [ 9526] [depth= 1] . ( 23 sec) [ -36720.1840] [ 9511] [depth= 1] . ( 23 sec) [ -36715.4121] [ 9512] [depth= 1] . ( 24 sec) [ -36712.3703] [ 9505] [depth= 2] . ( 24 sec) [ -36596.8365] [ 9492] [depth= 1] . ( 24 sec) [ -36591.5765] [ 9494] [depth= 1] . ( 24 sec) [ -36568.4743] [ 9494] [depth= 1] . ( 25 sec) [ -36566.4766] [ 9491] [depth= 1] . ( 26 sec) [ -35933.5856] [Branch lengths ] . ( 30 sec) [ -35776.6808] [GTR parameters ] . ( 30 sec) [ -35767.7006] [Alpha ][ 0.444200] . ( 31 sec) [ -35764.1076] [ 9491] [depth= 1] . ( 31 sec) [ -35761.6132] [ 9482] [depth= 2] . ( 31 sec) [ -35759.5792] [ 9486] [depth= 1] . ( 31 sec) [ -35755.2115] [ 9484] [depth= 1] . ( 32 sec) [ -35753.2478] [ 9486] [depth= 1] . ( 32 sec) [ -35726.0342] [ 9480] [depth= 11] . ( 32 sec) [ -35694.5497] [ 9456] [depth= 2] . ( 32 sec) [ -35680.7544] [ 9453] [depth= 2] . ( 32 sec) [ -35595.5808] [ 9425] [depth= 7] . ( 32 sec) [ -35589.2769] [ 9429] [depth= 4] . ( 33 sec) [ -35585.4826] [ 9420] [depth= 1] . ( 33 sec) [ -35582.3215] [ 9423] [depth= 1] . ( 34 sec) [ -35579.4865] [ 9416] [depth= 1] . ( 34 sec) [ -35563.4288] [ 9410] [depth= 6] . ( 34 sec) [ -35554.2912] [ 9397] [depth= 3] . ( 35 sec) [ -35547.9815] [ 9391] [depth= 1] . ( 35 sec) [ -35542.6064] [ 9387] [depth= 3] . ( 35 sec) [ -35539.4278] [ 9368] [depth= 6] . ( 35 sec) [ -35538.3273] [ 9366] [depth= 1] . ( 36 sec) [ -35535.0851] [ 9367] [depth= 1] . ( 36 sec) [ -35528.1421] [ 9367] [depth= 2] . ( 36 sec) [ -35524.3562] [ 9363] [depth= 1] . ( 38 sec) [ -35523.7972] [ 9361] [depth= 1] . ( 38 sec) [ -35523.5424] [ 9366] [depth= 1] . ( 38 sec) [ -35518.9703] [ 9371] [depth= 2] . ( 39 sec) [ -35516.8743] [ 9367] [depth= 1] . ( 39 sec) [ -35481.8300] [ 9347] [depth= 1] . ( 39 sec) [ -35463.5403] [ 9344] [depth= 4] . ( 39 sec) [ -35449.6772] [ 9336] [depth= 1] . ( 40 sec) [ -35440.8057] [ 9328] [depth= 1] . ( 40 sec) [ -35418.5139] [ 9331] [depth= 4] . ( 40 sec) [ -35418.1604] [ 9333] [depth= 1] . ( 40 sec) [ -35396.8642] [ 9328] [depth= 1] . ( 41 sec) [ -35396.6768] [ 9322] [depth= 2] . ( 41 sec) [ -35395.0156] [ 9317] [depth= 1] . ( 42 sec) [ -35388.9231] [ 9309] [depth= 1] . ( 42 sec) [ -35386.9339] [ 9312] [depth= 2] . ( 43 sec) [ -35372.5880] [ 9300] [depth= 1] . ( 43 sec) [ -35367.1108] [ 9303] [depth= 2] . ( 44 sec) [ -35345.4552] [ 9285] [depth= 3] . ( 44 sec) [ -35341.6230] [ 9288] [depth= 1] . ( 45 sec) [ -35335.1489] [ 9289] [depth= 1] . ( 46 sec) [ -35230.5668] [Branch lengths ] . ( 51 sec) [ -35220.8696] [GTR parameters ] . ( 51 sec) [ -35220.7189] [Alpha ][ 0.451233] . ( 52 sec) [ -35220.0950] [ 9286] [depth= 1] . ( 53 sec) [ -35218.6604] [ 9283] [depth= 1] . ( 53 sec) [ -35215.5847] [ 9278] [depth= 1] . ( 54 sec) [ -35215.0651] [ 9282] [depth= 1] . ( 55 sec) [ -35210.3368] [ 9292] [depth= 2] . ( 60 sec) [ -35208.6009] [ 9292] [depth= 1] . ( 65 sec) [ -35205.2730] [ 9294] [depth= 1] . ( 67 sec) [ -35177.3356] [Branch lengths ] . ( 71 sec) [ -35175.9426] [GTR parameters ] . ( 71 sec) [ -35175.8259] [Alpha ][ 0.457204] . ( 83 sec) [ -35175.7537] [ 9292] [depth= 1] . ( 87 sec) [ -35161.1982] [Branch lengths ] . ( 90 sec) [ -35159.9690] [GTR parameters ] . ( 91 sec) [ -35159.9644] [Alpha ][ 0.456019] . ( 106 sec) [ -35148.6030] [Branch lengths ] . ( 120 sec) [ -35147.6809] [ 9300] [depth= 2] . ( 120 sec) [ -35147.3286] [ 9304] [depth= 1] . ( 127 sec) [ -35146.1434] [ 9310] [depth= 1] . ( 132 sec) [ -35144.6841] [ 9303] [depth= 1] . ( 138 sec) [ -35144.6603] [ 9306] [depth= 1] . ( 194 sec) [ -35128.2232] [Branch lengths ] . ( 198 sec) [ -35126.4754] [GTR parameters ] . ( 198 sec) [ -35126.2030] [Alpha ][ 0.447589] . ( 224 sec) [ -35125.5933] [ 9303] [depth= 1] . ( 233 sec) [ -35125.1014] [ 9312] [depth= 3] . ( 288 sec) [ -35118.0759] [Branch lengths ] . ( 291 sec) [ -35117.6251] [GTR parameters ] . ( 291 sec) [ -35117.4853] [Alpha ][ 0.441675] . ( 382 sec) [ -35113.8792] [Branch lengths ] . ( 382 sec) [ -35113.8792] [Topology ] . ( 384 sec) [ -35112.9166] [Topology ] . ( 386 sec) [ -35112.4249] [Topology ] . ( 389 sec) [ -35112.0858] [Topology ] . ( 391 sec) [ -35111.8404] [Topology ] . ( 393 sec) [ -35111.6604] [Topology ] . ( 395 sec) [ -35111.4155] [Topology ] . ( 398 sec) [ -35110.8056] [Topology ] . ( 400 sec) [ -35110.5605] [Topology ] . ( 402 sec) [ -35110.4051] [Topology ] . ( 409 sec) [ -35108.9854] [GTR parameters ] . ( 409 sec) [ -35108.4647] [Alpha ][ 0.430963] . ( 409 sec) [ -35108.4647] [Topology ] . ( 411 sec) [ -35107.9722] [Topology ] . ( 414 sec) [ -35107.6616] [Topology ] . ( 416 sec) [ -35107.4422] [Topology ] . ( 418 sec) [ -35107.2858] [Topology ] . ( 421 sec) [ -35107.1736] [Topology ] . ( 423 sec) [ -35107.0933] [Topology ] . ( 425 sec) [ -35106.8928] [GTR parameters ] . ( 426 sec) [ -35106.7749] [Alpha ][ 0.426006] . ( 426 sec) [ -35106.7749] [Topology ] . ( 428 sec) [ -35106.6070] [Topology ] . ( 430 sec) [ -35106.4969] [Topology ] . ( 433 sec) [ -35106.4193] [Topology ] . ( 435 sec) [ -35106.3644] [Topology ] . ( 437 sec) [ -35106.3254] [Topology ] . ( 439 sec) [ -35106.2978] [Topology ] . ( 442 sec) [ -35106.2418] [GTR parameters ] . ( 442 sec) [ -35106.1998] [Alpha ][ 0.423090] . ( 442 sec) [ -35106.1998] [Topology ] . ( 444 sec) [ -35106.1446] [Topology ] . ( 447 sec) [ -35106.1085] [Topology ] . ( 449 sec) [ -35106.0833] [Topology ] . ( 451 sec) [ -35106.0655] [Topology ] . ( 454 sec) [ -35106.0530] [Topology ] . ( 456 sec) [ -35106.0442] [Topology ] . ( 458 sec) [ -35106.0268] [GTR parameters ] . ( 458 sec) [ -35106.0124] [Alpha ][ 0.421397] . ( 458 sec) [ -35106.0124] [Topology ] . ( 460 sec) [ -35105.9948] [Topology ] . ( 463 sec) [ -35105.9834] [Topology ] . ( 465 sec) [ -35105.9754] [Topology ] . ( 467 sec) [ -35105.9698] [Topology ] . ( 469 sec) [ -35105.9659] [Topology ] . ( 472 sec) [ -35105.9632] [Topology ] . ( 474 sec) [ -35105.9576] [GTR parameters ] . ( 474 sec) [ -35105.9529] [Alpha ][ 0.420432] . ( 474 sec) [ -35105.9529] [Topology ] . ( 476 sec) [ -35105.9473] [Topology ] . ( 478 sec) [ -35105.9437] [Topology ] . ( 481 sec) [ -35105.9412] [Topology ] . ( 483 sec) [ -35105.9395] [Topology ] . ( 485 sec) [ -35105.9383] [Topology ] . ( 488 sec) [ -35105.9374] [Topology ] . ( 489 sec) [ -35105.9358] [GTR parameters ] . ( 489 sec) [ -35105.9342] [Alpha ][ 0.419879] . ( 489 sec) [ -35105.9342] [Topology ] . ( 492 sec) [ -35105.9325] [Topology ] . ( 494 sec) [ -35105.9314] [Topology ] . ( 496 sec) [ -35105.9306] [Topology ] . ( 497 sec) [ -35105.9303] [GTR parameters ] . ( 498 sec) [ -35105.9303] [Alpha ][ 0.419879] . ( 498 sec) [ -35105.9303] [Topology ] . ( 500 sec) [ -35105.9296] [Topology ] . ( 501 sec) [ -35105.9296] [GTR parameters ] . ( 501 sec) [ -35105.9295] [Alpha ][ 0.419459] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35105.929464. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -56531.5608] [GTR parameters ] . ( 6 sec) [ -55327.3330] [Alpha ][ 0.500960] . ( 6 sec) [ -54865.5185] [13036] [depth= 4] . ( 6 sec) [ -54412.6686] [12973] [depth= 10] . ( 7 sec) [ -54292.4128] [12957] [depth= 6] . ( 7 sec) [ -54115.2222] [12959] [depth= 2] . ( 7 sec) [ -53939.9529] [12874] [depth= 4] . ( 7 sec) [ -53839.1377] [12846] [depth= 5] . ( 7 sec) [ -53828.2172] [12831] [depth= 3] . ( 7 sec) [ -53684.5229] [12781] [depth= 16] . ( 7 sec) [ -52532.4124] [12743] [depth= 6] . ( 8 sec) [ -52184.4261] [12678] [depth= 16] . ( 8 sec) [ -52038.3800] [12687] [depth= 7] . ( 8 sec) [ -51893.1906] [12621] [depth= 6] . ( 8 sec) [ -51826.3552] [12592] [depth= 2] . ( 8 sec) [ -51610.9656] [12555] [depth= 6] . ( 8 sec) [ -51605.7974] [12502] [depth= 3] . ( 8 sec) [ -51045.9790] [12489] [depth= 1] . ( 9 sec) [ -50813.1096] [12395] [depth= 18] . ( 9 sec) [ -50720.9008] [12377] [depth= 1] . ( 9 sec) [ -50609.5220] [12317] [depth= 18] . ( 9 sec) [ -50461.3733] [12313] [depth= 9] . ( 9 sec) [ -50243.4482] [12269] [depth= 2] . ( 9 sec) [ -49613.5466] [12163] [depth= 10] . ( 9 sec) [ -49512.9151] [12128] [depth= 6] . ( 10 sec) [ -49212.1900] [12080] [depth= 1] . ( 10 sec) [ -48236.2903] [11985] [depth= 7] . ( 10 sec) [ -46435.7439] [11942] [depth= 1] . ( 10 sec) [ -46238.1227] [11842] [depth= 18] . ( 10 sec) [ -45797.9275] [11818] [depth= 17] . ( 10 sec) [ -45507.4831] [11610] [depth= 19] . ( 10 sec) [ -45482.2082] [11616] [depth= 1] . ( 11 sec) [ -45383.7421] [11586] [depth= 4] . ( 11 sec) [ -45371.0481] [11639] [depth= 1] . ( 11 sec) [ -45147.3368] [11537] [depth= 5] . ( 11 sec) [ -45059.4552] [11484] [depth= 2] . ( 11 sec) [ -44947.2418] [11398] [depth= 8] . ( 11 sec) [ -44845.8514] [11387] [depth= 1] . ( 12 sec) [ -44663.8746] [11378] [depth= 2] . ( 12 sec) [ -44563.6136] [11404] [depth= 1] . ( 12 sec) [ -44517.3369] [11389] [depth= 1] . ( 12 sec) [ -44277.3021] [11344] [depth= 9] . ( 12 sec) [ -43964.2279] [11238] [depth= 6] . ( 12 sec) [ -43699.8088] [11188] [depth= 1] . ( 12 sec) [ -43495.6325] [11153] [depth= 12] . ( 13 sec) [ -43269.6212] [11068] [depth= 1] . ( 13 sec) [ -43196.9382] [11036] [depth= 6] . ( 13 sec) [ -42590.7273] [10987] [depth= 11] . ( 13 sec) [ -42442.6914] [10949] [depth= 9] . ( 13 sec) [ -42370.7587] [10914] [depth= 16] . ( 13 sec) [ -42336.1175] [10898] [depth= 1] . ( 13 sec) [ -42315.5644] [10899] [depth= 1] . ( 13 sec) [ -41820.8203] [10739] [depth= 13] . ( 14 sec) [ -41791.8705] [10820] [depth= 1] . ( 14 sec) [ -41671.7751] [10786] [depth= 8] . ( 14 sec) [ -41628.9741] [10782] [depth= 1] . ( 14 sec) [ -41467.8960] [10772] [depth= 1] . ( 14 sec) [ -40950.3789] [10722] [depth= 14] . ( 14 sec) [ -40907.9866] [10717] [depth= 6] . ( 14 sec) [ -40888.4952] [10712] [depth= 2] . ( 15 sec) [ -40830.1457] [10647] [depth= 16] . ( 15 sec) [ -40656.1457] [10584] [depth= 9] . ( 15 sec) [ -40543.0409] [10522] [depth= 11] . ( 15 sec) [ -40443.0778] [10507] [depth= 7] . ( 15 sec) [ -40351.0939] [10451] [depth= 8] . ( 15 sec) [ -40188.2412] [10410] [depth= 3] . ( 15 sec) [ -40165.5591] [10398] [depth= 1] . ( 16 sec) [ -40148.3477] [10394] [depth= 1] . ( 16 sec) [ -40056.1673] [10343] [depth= 8] . ( 16 sec) [ -39865.0829] [10321] [depth= 9] . ( 16 sec) [ -39782.3897] [10312] [depth= 1] . ( 16 sec) [ -39685.2207] [10300] [depth= 2] . ( 16 sec) [ -39673.4375] [10344] [depth= 1] . ( 17 sec) [ -39539.4347] [10237] [depth= 2] . ( 17 sec) [ -39405.4959] [10179] [depth= 2] . ( 17 sec) [ -39248.1230] [10130] [depth= 8] . ( 17 sec) [ -39227.6333] [10115] [depth= 1] . ( 17 sec) [ -38644.5013] [ 9982] [depth= 3] . ( 17 sec) [ -38616.1074] [ 9901] [depth= 1] . ( 18 sec) [ -38479.1571] [ 9897] [depth= 2] . ( 18 sec) [ -38443.4586] [ 9842] [depth= 2] . ( 18 sec) [ -38435.9188] [ 9845] [depth= 1] . ( 18 sec) [ -38426.6729] [ 9859] [depth= 3] . ( 18 sec) [ -38419.6360] [ 9848] [depth= 1] . ( 19 sec) [ -38398.1735] [ 9808] [depth= 7] . ( 19 sec) [ -38221.5575] [ 9800] [depth= 1] . ( 19 sec) [ -38119.1829] [ 9789] [depth= 1] . ( 19 sec) [ -38098.7433] [ 9787] [depth= 1] . ( 19 sec) [ -38085.5773] [ 9789] [depth= 1] . ( 19 sec) [ -38081.6905] [ 9785] [depth= 2] . ( 19 sec) [ -38070.2171] [ 9790] [depth= 1] . ( 20 sec) [ -37876.3853] [ 9720] [depth= 13] . ( 20 sec) [ -37828.7510] [ 9703] [depth= 2] . ( 20 sec) [ -37794.5617] [ 9689] [depth= 2] . ( 20 sec) [ -37677.6591] [ 9658] [depth= 1] . ( 20 sec) [ -37541.7601] [ 9627] [depth= 1] . ( 20 sec) [ -37455.5600] [ 9597] [depth= 2] . ( 20 sec) [ -37423.6595] [ 9591] [depth= 1] . ( 21 sec) [ -37417.2532] [ 9591] [depth= 2] . ( 21 sec) [ -37416.8086] [ 9583] [depth= 1] . ( 21 sec) [ -37282.9594] [ 9563] [depth= 6] . ( 21 sec) [ -37262.8634] [ 9530] [depth= 4] . ( 21 sec) [ -37074.7938] [ 9510] [depth= 5] . ( 21 sec) [ -37065.7506] [ 9591] [depth= 1] . ( 21 sec) [ -37000.5434] [ 9510] [depth= 1] . ( 22 sec) [ -36812.5190] [ 9463] [depth= 1] . ( 22 sec) [ -36795.7122] [ 9461] [depth= 4] . ( 22 sec) [ -36760.4773] [ 9472] [depth= 1] . ( 22 sec) [ -36699.5844] [ 9458] [depth= 2] . ( 22 sec) [ -36683.4201] [ 9443] [depth= 3] . ( 23 sec) [ -36682.5469] [ 9449] [depth= 1] . ( 23 sec) [ -36651.4722] [ 9447] [depth= 1] . ( 23 sec) [ -36538.1091] [ 9449] [depth= 1] . ( 23 sec) [ -36507.5107] [ 9435] [depth= 2] . ( 23 sec) [ -36495.1341] [ 9436] [depth= 1] . ( 24 sec) [ -36492.6217] [ 9437] [depth= 1] . ( 24 sec) [ -36462.3922] [ 9442] [depth= 1] . ( 24 sec) [ -36406.8839] [ 9436] [depth= 1] . ( 24 sec) [ -36384.3522] [ 9424] [depth= 3] . ( 25 sec) [ -36381.0680] [ 9430] [depth= 1] . ( 25 sec) [ -36353.0731] [ 9432] [depth= 1] . ( 25 sec) [ -36338.6822] [ 9436] [depth= 1] . ( 25 sec) [ -36326.7335] [ 9436] [depth= 1] . ( 26 sec) [ -35745.3759] [Branch lengths ] . ( 31 sec) [ -35584.5045] [GTR parameters ] . ( 31 sec) [ -35574.3448] [Alpha ][ 0.440225] . ( 31 sec) [ -35568.2744] [ 9432] [depth= 1] . ( 32 sec) [ -35567.8027] [ 9430] [depth= 1] . ( 33 sec) [ -35559.2425] [ 9390] [depth= 8] . ( 33 sec) [ -35549.2765] [ 9368] [depth= 3] . ( 33 sec) [ -35504.1372] [ 9343] [depth= 1] . ( 34 sec) [ -35503.1227] [ 9344] [depth= 1] . ( 34 sec) [ -35502.7390] [ 9346] [depth= 1] . ( 34 sec) [ -35501.8534] [ 9347] [depth= 1] . ( 35 sec) [ -35499.5040] [ 9344] [depth= 1] . ( 35 sec) [ -35498.4957] [ 9336] [depth= 1] . ( 36 sec) [ -35493.3202] [ 9334] [depth= 1] . ( 37 sec) [ -35487.2041] [ 9322] [depth= 2] . ( 37 sec) [ -35484.4854] [ 9321] [depth= 1] . ( 38 sec) [ -35468.0540] [ 9319] [depth= 1] . ( 38 sec) [ -35466.9070] [ 9318] [depth= 1] . ( 38 sec) [ -35465.6120] [ 9322] [depth= 1] . ( 39 sec) [ -35460.1744] [ 9315] [depth= 2] . ( 39 sec) [ -35460.0830] [ 9311] [depth= 1] . ( 40 sec) [ -35459.5883] [ 9313] [depth= 1] . ( 41 sec) [ -35458.8875] [ 9317] [depth= 4] . ( 41 sec) [ -35432.7444] [ 9313] [depth= 1] . ( 41 sec) [ -35430.6964] [ 9309] [depth= 1] . ( 42 sec) [ -35430.0135] [ 9313] [depth= 1] . ( 43 sec) [ -35429.8268] [ 9309] [depth= 1] . ( 43 sec) [ -35421.9907] [ 9308] [depth= 2] . ( 43 sec) [ -35409.1724] [ 9309] [depth= 2] . ( 44 sec) [ -35391.8627] [ 9298] [depth= 3] . ( 45 sec) [ -35391.2868] [ 9300] [depth= 2] . ( 45 sec) [ -35390.3050] [ 9302] [depth= 1] . ( 46 sec) [ -35388.2457] [ 9298] [depth= 1] . ( 46 sec) [ -35382.8498] [ 9302] [depth= 1] . ( 46 sec) [ -35375.6480] [ 9306] [depth= 1] . ( 48 sec) [ -35265.6457] [Branch lengths ] . ( 52 sec) [ -35259.3475] [GTR parameters ] . ( 52 sec) [ -35259.1832] [Alpha ][ 0.447407] . ( 53 sec) [ -35255.7916] [ 9305] [depth= 1] . ( 55 sec) [ -35253.4635] [ 9300] [depth= 1] . ( 58 sec) [ -35249.6744] [ 9289] [depth= 1] . ( 59 sec) [ -35248.3519] [ 9291] [depth= 1] . ( 69 sec) [ -35201.4689] [Branch lengths ] . ( 72 sec) [ -35200.1826] [GTR parameters ] . ( 73 sec) [ -35200.0500] [Alpha ][ 0.453725] . ( 75 sec) [ -35196.9612] [ 9295] [depth= 1] . ( 81 sec) [ -35196.1817] [ 9288] [depth= 1] . ( 91 sec) [ -35165.0640] [Branch lengths ] . ( 93 sec) [ -35163.5191] [GTR parameters ] . ( 94 sec) [ -35163.5154] [Alpha ][ 0.454728] . ( 110 sec) [ -35152.2750] [Branch lengths ] . ( 114 sec) [ -35152.2557] [ 9283] [depth= 1] . ( 134 sec) [ -35150.7801] [ 9296] [depth= 2] . ( 136 sec) [ -35150.7133] [ 9301] [depth= 1] . ( 145 sec) [ -35150.1893] [ 9312] [depth= 2] . ( 150 sec) [ -35149.7243] [ 9303] [depth= 1] . ( 187 sec) [ -35148.5582] [ 9297] [depth= 1] . ( 191 sec) [ -35148.5040] [ 9300] [depth= 1] . ( 192 sec) [ -35147.3740] [ 9306] [depth= 2] . ( 194 sec) [ -35130.3311] [Branch lengths ] . ( 198 sec) [ -35128.9272] [GTR parameters ] . ( 199 sec) [ -35128.6093] [Alpha ][ 0.445697] . ( 282 sec) [ -35128.4568] [ 9303] [depth= 1] . ( 286 sec) [ -35122.7202] [Branch lengths ] . ( 288 sec) [ -35122.3357] [GTR parameters ] . ( 288 sec) [ -35122.2222] [Alpha ][ 0.440448] . ( 378 sec) [ -35119.0377] [Branch lengths ] . ( 378 sec) [ -35119.0377] [Topology ] . ( 380 sec) [ -35117.2193] [Topology ] . ( 382 sec) [ -35114.3198] [Topology ] . ( 385 sec) [ -35113.2608] [Topology ] . ( 387 sec) [ -35112.7627] [Topology ] . ( 389 sec) [ -35112.5006] [Topology ] . ( 392 sec) [ -35112.1512] [Topology ] . ( 394 sec) [ -35111.4782] [Topology ] . ( 396 sec) [ -35111.2406] [Topology ] . ( 399 sec) [ -35111.1051] [Topology ] . ( 403 sec) [ -35109.9435] [GTR parameters ] . ( 404 sec) [ -35109.4031] [Alpha ][ 0.429638] . ( 404 sec) [ -35109.4031] [Topology ] . ( 406 sec) [ -35108.9830] [Topology ] . ( 408 sec) [ -35108.7244] [Topology ] . ( 411 sec) [ -35108.5438] [Topology ] . ( 413 sec) [ -35108.4157] [Topology ] . ( 415 sec) [ -35108.3244] [Topology ] . ( 417 sec) [ -35108.2595] [Topology ] . ( 420 sec) [ -35108.0805] [GTR parameters ] . ( 421 sec) [ -35107.9749] [Alpha ][ 0.424979] . ( 421 sec) [ -35107.9749] [Topology ] . ( 423 sec) [ -35107.8311] [Topology ] . ( 425 sec) [ -35107.7375] [Topology ] . ( 428 sec) [ -35107.6719] [Topology ] . ( 430 sec) [ -35107.6255] [Topology ] . ( 432 sec) [ -35107.5927] [Topology ] . ( 434 sec) [ -35107.5695] [Topology ] . ( 436 sec) [ -35107.5227] [GTR parameters ] . ( 436 sec) [ -35107.4843] [Alpha ][ 0.422206] . ( 436 sec) [ -35107.4843] [Topology ] . ( 439 sec) [ -35107.4378] [Topology ] . ( 441 sec) [ -35107.4076] [Topology ] . ( 443 sec) [ -35107.3865] [Topology ] . ( 445 sec) [ -35107.3716] [Topology ] . ( 448 sec) [ -35107.3611] [Topology ] . ( 450 sec) [ -35107.3537] [Topology ] . ( 453 sec) [ -35107.3337] [GTR parameters ] . ( 453 sec) [ -35107.3215] [Alpha ][ 0.420655] . ( 453 sec) [ -35107.3215] [Topology ] . ( 456 sec) [ -35107.3051] [Topology ] . ( 458 sec) [ -35107.2943] [Topology ] . ( 460 sec) [ -35107.2868] [Topology ] . ( 463 sec) [ -35107.2816] [Topology ] . ( 465 sec) [ -35107.2779] [Topology ] . ( 467 sec) [ -35107.2753] [Topology ] . ( 469 sec) [ -35107.2705] [GTR parameters ] . ( 469 sec) [ -35107.2662] [Alpha ][ 0.419737] . ( 469 sec) [ -35107.2662] [Topology ] . ( 471 sec) [ -35107.2611] [Topology ] . ( 473 sec) [ -35107.2579] [Topology ] . ( 476 sec) [ -35107.2556] [Topology ] . ( 478 sec) [ -35107.2540] [Topology ] . ( 480 sec) [ -35107.2529] [Topology ] . ( 483 sec) [ -35107.2521] [Topology ] . ( 484 sec) [ -35107.2498] [GTR parameters ] . ( 484 sec) [ -35107.2483] [Alpha ][ 0.419185] . ( 484 sec) [ -35107.2483] [Topology ] . ( 487 sec) [ -35107.2465] [Topology ] . ( 489 sec) [ -35107.2453] [Topology ] . ( 491 sec) [ -35107.2446] [Topology ] . ( 492 sec) [ -35107.2442] [GTR parameters ] . ( 492 sec) [ -35107.2442] [Alpha ][ 0.419185] . ( 492 sec) [ -35107.2442] [Topology ] . ( 495 sec) [ -35107.2435] [Topology ] . ( 495 sec) [ -35107.2435] [GTR parameters ] . ( 495 sec) [ -35107.2433] [Alpha ][ 0.418765] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35107.243331. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -54119.9023] [GTR parameters ] . ( 4 sec) [ -52963.9083] [Alpha ][ 0.500960] . ( 4 sec) [ -52813.1027] [12898] [depth= 8] . ( 5 sec) [ -52629.7666] [12808] [depth= 8] . ( 5 sec) [ -52502.7343] [12784] [depth= 2] . ( 5 sec) [ -52259.5864] [12742] [depth= 1] . ( 5 sec) [ -52059.4187] [12618] [depth= 3] . ( 5 sec) [ -51995.7726] [12592] [depth= 9] . ( 5 sec) [ -51226.8300] [12592] [depth= 2] . ( 6 sec) [ -51160.5583] [12567] [depth= 2] . ( 6 sec) [ -51079.1021] [12548] [depth= 2] . ( 6 sec) [ -50941.1924] [12506] [depth= 9] . ( 6 sec) [ -50886.4208] [12477] [depth= 1] . ( 6 sec) [ -50739.3327] [12467] [depth= 7] . ( 6 sec) [ -50719.7293] [12460] [depth= 1] . ( 7 sec) [ -50632.5855] [12477] [depth= 1] . ( 7 sec) [ -50601.3387] [12454] [depth= 9] . ( 7 sec) [ -50554.0529] [12445] [depth= 1] . ( 7 sec) [ -50530.4367] [12435] [depth= 3] . ( 7 sec) [ -50215.2246] [12432] [depth= 1] . ( 7 sec) [ -50103.8031] [12414] [depth= 6] . ( 8 sec) [ -49928.4292] [12397] [depth= 7] . ( 8 sec) [ -49728.4304] [12304] [depth= 12] . ( 8 sec) [ -49549.4841] [12201] [depth= 2] . ( 8 sec) [ -49258.0561] [12137] [depth= 14] . ( 8 sec) [ -49151.7447] [12055] [depth= 8] . ( 8 sec) [ -49026.0106] [12034] [depth= 3] . ( 8 sec) [ -48984.4031] [12077] [depth= 1] . ( 9 sec) [ -48702.4925] [12001] [depth= 5] . ( 9 sec) [ -48622.2808] [11886] [depth= 1] . ( 9 sec) [ -48612.8251] [11868] [depth= 1] . ( 9 sec) [ -48455.2112] [11834] [depth= 7] . ( 9 sec) [ -48322.6924] [11808] [depth= 6] . ( 9 sec) [ -48267.0617] [11803] [depth= 4] . ( 9 sec) [ -48164.0982] [11750] [depth= 4] . ( 10 sec) [ -48132.4343] [11749] [depth= 2] . ( 10 sec) [ -47609.3649] [11634] [depth= 1] . ( 10 sec) [ -47604.7526] [11622] [depth= 11] . ( 10 sec) [ -47508.7299] [11551] [depth= 7] . ( 10 sec) [ -47447.3034] [11536] [depth= 4] . ( 10 sec) [ -47344.8202] [11481] [depth= 14] . ( 10 sec) [ -47307.6335] [11459] [depth= 1] . ( 11 sec) [ -46818.0679] [11381] [depth= 13] . ( 11 sec) [ -46773.7395] [11361] [depth= 12] . ( 11 sec) [ -46660.2620] [11281] [depth= 3] . ( 11 sec) [ -46631.9887] [11278] [depth= 1] . ( 11 sec) [ -46470.6985] [11214] [depth= 7] . ( 11 sec) [ -46132.3645] [11134] [depth= 1] . ( 12 sec) [ -46001.7207] [11095] [depth= 10] . ( 12 sec) [ -45593.5893] [11044] [depth= 9] . ( 12 sec) [ -45393.1743] [10984] [depth= 3] . ( 12 sec) [ -45370.3444] [10962] [depth= 5] . ( 12 sec) [ -45353.7826] [10964] [depth= 1] . ( 12 sec) [ -45332.4957] [10952] [depth= 6] . ( 13 sec) [ -45228.7140] [10927] [depth= 11] . ( 13 sec) [ -45023.5757] [10842] [depth= 13] . ( 13 sec) [ -44941.0896] [10829] [depth= 7] . ( 13 sec) [ -42832.7114] [10754] [depth= 11] . ( 13 sec) [ -42787.5268] [10742] [depth= 10] . ( 13 sec) [ -42255.0538] [10718] [depth= 8] . ( 14 sec) [ -42035.3154] [10651] [depth= 3] . ( 14 sec) [ -41940.1810] [10605] [depth= 2] . ( 14 sec) [ -41899.4068] [10597] [depth= 2] . ( 14 sec) [ -41682.3288] [10544] [depth= 10] . ( 14 sec) [ -41459.9231] [10509] [depth= 1] . ( 14 sec) [ -41455.5099] [10512] [depth= 1] . ( 15 sec) [ -41432.3715] [10458] [depth= 1] . ( 15 sec) [ -41095.9636] [10387] [depth= 5] . ( 15 sec) [ -41080.8062] [10377] [depth= 1] . ( 15 sec) [ -40996.0102] [10336] [depth= 7] . ( 15 sec) [ -40857.8522] [10339] [depth= 4] . ( 16 sec) [ -40849.9501] [10342] [depth= 1] . ( 16 sec) [ -40813.6731] [10308] [depth= 3] . ( 16 sec) [ -40797.5882] [10303] [depth= 2] . ( 16 sec) [ -40714.0426] [10288] [depth= 1] . ( 16 sec) [ -40651.5373] [10268] [depth= 9] . ( 16 sec) [ -40595.1019] [10257] [depth= 11] . ( 17 sec) [ -40258.0293] [10239] [depth= 6] . ( 17 sec) [ -40212.5076] [10223] [depth= 2] . ( 17 sec) [ -40165.3702] [10196] [depth= 3] . ( 17 sec) [ -40053.4584] [10189] [depth= 1] . ( 17 sec) [ -40019.4121] [10169] [depth= 4] . ( 18 sec) [ -39983.1590] [10170] [depth= 1] . ( 18 sec) [ -39766.1354] [10149] [depth= 1] . ( 18 sec) [ -39682.1401] [10133] [depth= 1] . ( 18 sec) [ -39598.0659] [10096] [depth= 9] . ( 18 sec) [ -39456.1277] [10014] [depth= 6] . ( 18 sec) [ -39399.0512] [ 9971] [depth= 1] . ( 19 sec) [ -39375.6350] [ 9956] [depth= 1] . ( 19 sec) [ -38960.1424] [ 9958] [depth= 2] . ( 19 sec) [ -38804.1545] [ 9947] [depth= 10] . ( 19 sec) [ -38681.9171] [ 9917] [depth= 1] . ( 19 sec) [ -38591.2398] [ 9916] [depth= 1] . ( 19 sec) [ -38584.1843] [ 9913] [depth= 1] . ( 20 sec) [ -38236.6482] [ 9781] [depth= 5] . ( 20 sec) [ -38223.3425] [ 9770] [depth= 1] . ( 20 sec) [ -38055.6892] [ 9720] [depth= 8] . ( 20 sec) [ -38014.0814] [ 9708] [depth= 4] . ( 21 sec) [ -37972.8855] [ 9681] [depth= 3] . ( 21 sec) [ -37968.0778] [ 9681] [depth= 1] . ( 22 sec) [ -37965.1533] [ 9679] [depth= 1] . ( 22 sec) [ -37934.7357] [ 9657] [depth= 2] . ( 22 sec) [ -37318.2297] [ 9658] [depth= 2] . ( 22 sec) [ -37301.8037] [ 9641] [depth= 2] . ( 22 sec) [ -37029.5174] [ 9627] [depth= 1] . ( 22 sec) [ -36968.7007] [ 9615] [depth= 1] . ( 23 sec) [ -36949.6744] [ 9622] [depth= 1] . ( 23 sec) [ -36944.6295] [ 9618] [depth= 2] . ( 23 sec) [ -36902.6685] [ 9615] [depth= 3] . ( 23 sec) [ -36885.3888] [ 9611] [depth= 1] . ( 24 sec) [ -36883.8286] [ 9614] [depth= 1] . ( 24 sec) [ -36863.2061] [ 9606] [depth= 1] . ( 24 sec) [ -36845.2505] [ 9607] [depth= 1] . ( 24 sec) [ -36742.0845] [ 9565] [depth= 10] . ( 24 sec) [ -36673.1284] [ 9552] [depth= 6] . ( 25 sec) [ -36660.2585] [ 9552] [depth= 3] . ( 25 sec) [ -36651.8566] [ 9545] [depth= 4] . ( 25 sec) [ -36647.0970] [ 9544] [depth= 2] . ( 26 sec) [ -36644.4839] [ 9551] [depth= 2] . ( 26 sec) [ -36642.0470] [ 9556] [depth= 1] . ( 26 sec) [ -36641.7422] [ 9558] [depth= 2] . ( 26 sec) [ -36627.5329] [ 9542] [depth= 1] . ( 27 sec) [ -36024.5969] [Branch lengths ] . ( 32 sec) [ -35865.4222] [GTR parameters ] . ( 32 sec) [ -35857.1873] [Alpha ][ 0.445913] . ( 32 sec) [ -35755.8141] [ 9499] [depth= 8] . ( 33 sec) [ -35617.5931] [ 9467] [depth= 5] . ( 33 sec) [ -35613.9959] [ 9459] [depth= 1] . ( 33 sec) [ -35529.2716] [ 9385] [depth= 4] . ( 33 sec) [ -35526.4565] [ 9374] [depth= 1] . ( 33 sec) [ -35524.5123] [ 9375] [depth= 1] . ( 34 sec) [ -35523.7007] [ 9366] [depth= 2] . ( 35 sec) [ -35522.8065] [ 9369] [depth= 2] . ( 35 sec) [ -35520.4253] [ 9377] [depth= 1] . ( 36 sec) [ -35519.1747] [ 9376] [depth= 1] . ( 36 sec) [ -35513.9305] [ 9378] [depth= 1] . ( 36 sec) [ -35509.8502] [ 9376] [depth= 1] . ( 36 sec) [ -35508.7074] [ 9379] [depth= 2] . ( 37 sec) [ -35496.2691] [ 9358] [depth= 4] . ( 37 sec) [ -35487.6025] [ 9351] [depth= 1] . ( 38 sec) [ -35482.6964] [ 9346] [depth= 1] . ( 38 sec) [ -35482.3200] [ 9348] [depth= 1] . ( 39 sec) [ -35462.0949] [ 9344] [depth= 4] . ( 40 sec) [ -35460.8724] [ 9351] [depth= 2] . ( 41 sec) [ -35413.3616] [ 9333] [depth= 1] . ( 41 sec) [ -35391.6818] [ 9325] [depth= 5] . ( 41 sec) [ -35386.2879] [ 9321] [depth= 2] . ( 42 sec) [ -35381.0649] [ 9312] [depth= 2] . ( 43 sec) [ -35364.2438] [ 9308] [depth= 6] . ( 44 sec) [ -35363.6948] [ 9303] [depth= 3] . ( 44 sec) [ -35361.1016] [ 9305] [depth= 1] . ( 45 sec) [ -35351.4913] [ 9305] [depth= 1] . ( 45 sec) [ -35349.1054] [ 9304] [depth= 1] . ( 45 sec) [ -35348.4379] [ 9308] [depth= 1] . ( 46 sec) [ -35347.5969] [ 9306] [depth= 2] . ( 47 sec) [ -35335.2728] [ 9297] [depth= 1] . ( 49 sec) [ -35215.4286] [Branch lengths ] . ( 53 sec) [ -35206.6770] [GTR parameters ] . ( 53 sec) [ -35206.5248] [Alpha ][ 0.452901] . ( 56 sec) [ -35205.7627] [ 9298] [depth= 3] . ( 61 sec) [ -35204.0942] [ 9293] [depth= 2] . ( 65 sec) [ -35203.7426] [ 9293] [depth= 1] . ( 67 sec) [ -35173.7981] [Branch lengths ] . ( 72 sec) [ -35172.0205] [GTR parameters ] . ( 72 sec) [ -35171.8879] [Alpha ][ 0.459159] . ( 73 sec) [ -35171.6416] [ 9298] [depth= 1] . ( 76 sec) [ -35171.3116] [ 9299] [depth= 1] . ( 88 sec) [ -35154.9998] [Branch lengths ] . ( 91 sec) [ -35153.8971] [GTR parameters ] . ( 91 sec) [ -35153.8568] [Alpha ][ 0.455780] . ( 109 sec) [ -35142.1215] [Branch lengths ] . ( 152 sec) [ -35141.4097] [ 9294] [depth= 1] . ( 195 sec) [ -35140.6494] [ 9302] [depth= 1] . ( 197 sec) [ -35130.7443] [Branch lengths ] . ( 201 sec) [ -35129.1168] [GTR parameters ] . ( 201 sec) [ -35128.6750] [Alpha ][ 0.445292] . ( 255 sec) [ -35126.0818] [ 9306] [depth= 1] . ( 292 sec) [ -35119.0814] [Branch lengths ] . ( 296 sec) [ -35118.7019] [GTR parameters ] . ( 296 sec) [ -35118.5064] [Alpha ][ 0.438546] . ( 340 sec) [ -35118.3339] [ 9299] [depth= 1] . ( 346 sec) [ -35118.2570] [ 9307] [depth= 3] . ( 386 sec) [ -35113.8334] [Branch lengths ] . ( 389 sec) [ -35113.6548] [GTR parameters ] . ( 389 sec) [ -35113.5871] [Alpha ][ 0.434613] . ( 393 sec) [ -35112.9735] [ 9311] [depth= 2] . ( 418 sec) [ -35112.8265] [ 9310] [depth= 1] . ( 476 sec) [ -35109.4538] [Branch lengths ] . ( 479 sec) [ -35109.3279] [GTR parameters ] . ( 479 sec) [ -35109.2755] [Alpha ][ 0.431208] . ( 567 sec) [ -35107.8946] [Branch lengths ] . ( 567 sec) [ -35107.8946] [Topology ] . ( 569 sec) [ -35107.5296] [Topology ] . ( 571 sec) [ -35107.3462] [Topology ] . ( 574 sec) [ -35107.2211] [Topology ] . ( 576 sec) [ -35107.1325] [Topology ] . ( 578 sec) [ -35107.0694] [Topology ] . ( 581 sec) [ -35107.0244] [Topology ] . ( 584 sec) [ -35106.7908] [GTR parameters ] . ( 584 sec) [ -35106.6325] [Alpha ][ 0.425478] . ( 584 sec) [ -35106.6325] [Topology ] . ( 586 sec) [ -35106.4922] [Topology ] . ( 589 sec) [ -35106.4027] [Topology ] . ( 591 sec) [ -35106.3401] [Topology ] . ( 593 sec) [ -35106.2958] [Topology ] . ( 596 sec) [ -35106.2645] [Topology ] . ( 598 sec) [ -35106.2423] [Topology ] . ( 601 sec) [ -35106.1909] [GTR parameters ] . ( 601 sec) [ -35106.1544] [Alpha ][ 0.422767] . ( 601 sec) [ -35106.1544] [Topology ] . ( 604 sec) [ -35106.1085] [Topology ] . ( 606 sec) [ -35106.0787] [Topology ] . ( 608 sec) [ -35106.0578] [Topology ] . ( 611 sec) [ -35106.0432] [Topology ] . ( 613 sec) [ -35106.0329] [Topology ] . ( 615 sec) [ -35106.0257] [Topology ] . ( 617 sec) [ -35106.0105] [GTR parameters ] . ( 618 sec) [ -35105.9984] [Alpha ][ 0.421216] . ( 618 sec) [ -35105.9984] [Topology ] . ( 620 sec) [ -35105.9836] [Topology ] . ( 622 sec) [ -35105.9741] [Topology ] . ( 625 sec) [ -35105.9675] [Topology ] . ( 627 sec) [ -35105.9628] [Topology ] . ( 629 sec) [ -35105.9596] [Topology ] . ( 632 sec) [ -35105.9573] [Topology ] . ( 635 sec) [ -35105.9526] [GTR parameters ] . ( 635 sec) [ -35105.9486] [Alpha ][ 0.420326] . ( 635 sec) [ -35105.9486] [Topology ] . ( 637 sec) [ -35105.9439] [Topology ] . ( 640 sec) [ -35105.9410] [Topology ] . ( 642 sec) [ -35105.9389] [Topology ] . ( 644 sec) [ -35105.9375] [Topology ] . ( 647 sec) [ -35105.9365] [Topology ] . ( 649 sec) [ -35105.9358] [Topology ] . ( 650 sec) [ -35105.9343] [GTR parameters ] . ( 651 sec) [ -35105.9331] [Alpha ][ 0.419820] . ( 651 sec) [ -35105.9331] [Topology ] . ( 653 sec) [ -35105.9316] [Topology ] . ( 655 sec) [ -35105.9306] [Topology ] . ( 656 sec) [ -35105.9305] [GTR parameters ] . ( 656 sec) [ -35105.9305] [Alpha ][ 0.419820] . ( 657 sec) [ -35105.9305] [Topology ] . ( 659 sec) [ -35105.9297] [Topology ] . ( 659 sec) [ -35105.9297] [GTR parameters ] . ( 660 sec) [ -35105.9297] [Alpha ][ 0.419820] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35105.929679. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -36495.9506] [GTR parameters ] . ( 5 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 5 sec) [ -36002.5932] [Topology ] . ( 7 sec) [ -35423.6231] [Topology ] . ( 10 sec) [ -35317.4470] [Topology ] . ( 12 sec) [ -35293.7583] [Topology ] . ( 14 sec) [ -35285.1407] [Topology ] . ( 16 sec) [ -35280.7055] [Topology ] . ( 19 sec) [ -35278.0935] [Topology ] . ( 21 sec) [ -35276.2739] [Topology ] . ( 23 sec) [ -35275.3266] [Topology ] . ( 25 sec) [ -35274.2363] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -35272.9942] [Topology ] . ( 54 sec) [ -35208.5581] [GTR parameters ] . ( 54 sec) [ -35204.6841] [Alpha ][ 0.464402] . ( 54 sec) [ -35204.6841] [Topology ] . ( 57 sec) [ -35193.4410] [Topology ] . ( 59 sec) [ -35186.4924] [Topology ] . ( 61 sec) [ -35181.2926] [Topology ] . ( 63 sec) [ -35177.0730] [Topology ] . ( 66 sec) [ -35173.4542] [Topology ] . ( 68 sec) [ -35170.3629] [Topology ] . ( 70 sec) [ -35167.7702] [Topology ] . ( 72 sec) [ -35165.6380] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -35155.5880] [GTR parameters ] . ( 98 sec) [ -35155.2055] [Alpha ][ 0.454189] . ( 98 sec) [ -35155.2055] [Topology ] . ( 101 sec) [ -35150.8159] [Topology ] . ( 103 sec) [ -35147.8747] [Topology ] . ( 105 sec) [ -35145.7696] [Topology ] . ( 107 sec) [ -35144.2357] [Topology ] . ( 110 sec) [ -35143.1072] [Topology ] . ( 112 sec) [ -35142.2702] [Topology ] . Checking for NNIs, optimizing five branches... . ( 137 sec) [ -35140.5502] [GTR parameters ] . ( 137 sec) [ -35140.0006] [Alpha ][ 0.442745] . ( 137 sec) [ -35140.0006] [Topology ] . ( 139 sec) [ -35138.4908] [Topology ] . ( 142 sec) [ -35137.4503] [Topology ] . ( 144 sec) [ -35136.6902] [Topology ] . ( 146 sec) [ -35136.1303] [Topology ] . ( 148 sec) [ -35135.7172] [Topology ] . ( 151 sec) [ -35135.4120] [Topology ] . Checking for NNIs, optimizing five branches... . ( 172 sec) [ -35135.3839] [Topology ] . ( 176 sec) [ -35134.7559] [GTR parameters ] . ( 177 sec) [ -35134.4189] [Alpha ][ 0.434211] . ( 177 sec) [ -35134.4189] [Topology ] . ( 179 sec) [ -35128.0537] [Topology ] . ( 181 sec) [ -35126.6368] [Topology ] . ( 183 sec) [ -35126.3037] [Topology ] . ( 186 sec) [ -35126.1149] [Topology ] . ( 188 sec) [ -35125.9887] [Topology ] . ( 190 sec) [ -35125.9007] [Topology ] . ( 193 sec) [ -35125.8389] [Topology ] . Checking for NNIs, optimizing five branches... . ( 216 sec) [ -35125.6522] [GTR parameters ] . ( 217 sec) [ -35125.4511] [Alpha ][ 0.427834] . ( 217 sec) [ -35125.4511] [Topology ] . ( 219 sec) [ -35125.2913] [Topology ] . ( 221 sec) [ -35125.1900] [Topology ] . ( 223 sec) [ -35125.1191] [Topology ] . ( 226 sec) [ -35125.0689] [Topology ] . ( 228 sec) [ -35125.0332] [Topology ] . ( 230 sec) [ -35125.0077] [Topology ] . Checking for NNIs, optimizing five branches... . ( 254 sec) [ -35124.9480] [GTR parameters ] . ( 254 sec) [ -35124.9013] [Alpha ][ 0.424805] . ( 254 sec) [ -35124.9013] [Topology ] . ( 256 sec) [ -35124.8461] [Topology ] . ( 259 sec) [ -35124.8103] [Topology ] . ( 261 sec) [ -35124.7850] [Topology ] . ( 263 sec) [ -35124.7670] [Topology ] . ( 266 sec) [ -35124.7541] [Topology ] . ( 268 sec) [ -35124.7449] [Topology ] . Checking for NNIs, optimizing five branches... . ( 291 sec) [ -35124.7299] [GTR parameters ] . ( 291 sec) [ -35124.7141] [Alpha ][ 0.423056] . ( 291 sec) [ -35124.7141] [Topology ] . ( 293 sec) [ -35124.6957] [Topology ] . ( 296 sec) [ -35124.6836] [Topology ] . ( 298 sec) [ -35124.6750] [Topology ] . ( 301 sec) [ -35124.6688] [Topology ] . ( 303 sec) [ -35124.6644] [Topology ] . ( 305 sec) [ -35124.6612] [Topology ] . Checking for NNIs, optimizing five branches... . ( 328 sec) [ -35124.6565] [GTR parameters ] . ( 328 sec) [ -35124.6511] [Alpha ][ 0.422039] . ( 328 sec) [ -35124.6511] [Topology ] . ( 330 sec) [ -35124.6451] [Topology ] . ( 333 sec) [ -35124.6411] [Topology ] . ( 335 sec) [ -35124.6382] [Topology ] . ( 337 sec) [ -35124.6362] [Topology ] . ( 340 sec) [ -35124.6348] [Topology ] . ( 342 sec) [ -35124.6337] [Topology ] . Checking for NNIs, optimizing five branches... . ( 365 sec) [ -35124.6310] [GTR parameters ] . ( 365 sec) [ -35124.6295] [Alpha ][ 0.421498] . ( 365 sec) [ -35124.6295] [Topology ] . ( 367 sec) [ -35124.6275] [Topology ] . ( 370 sec) [ -35124.6261] [Topology ] . ( 372 sec) [ -35124.6251] [Topology ] . Checking for NNIs, optimizing five branches... . ( 394 sec) [ -35124.6243] [GTR parameters ] . ( 394 sec) [ -35124.6243] [Alpha ][ 0.421077] . ( 394 sec) [ -35124.6243] [Topology ] . ( 396 sec) [ -35124.6228] [Topology ] . ( 398 sec) [ -35124.6219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 420 sec) [ -35124.6216] [GTR parameters ] . ( 420 sec) [ -35124.6216] [Alpha ][ 0.421077] . ( 420 sec) [ -35124.6216] [Topology ] . ( 423 sec) [ -35124.6208] [Topology ] . Checking for NNIs, optimizing five branches... . ( 445 sec) [ -35124.6208] [GTR parameters ] . ( 445 sec) [ -35124.6208] [Alpha ][ 0.421077] . ( 445 sec) [ -35124.6208] [Topology ] . ( 447 sec) [ -35124.6201] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 495 sec) [ -36495.9506] [GTR parameters ] . ( 495 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 497 sec) [ -35998.6346] [ 9298] [depth= 1] . ( 498 sec) [ -35996.9518] [ 9294] [depth= 1] . ( 498 sec) [ -35993.4197] [ 9298] [depth= 1] . ( 499 sec) [ -35990.0069] [ 9296] [depth= 1] . ( 500 sec) [ -35989.6571] [ 9298] [depth= 1] . ( 500 sec) [ -35988.6791] [ 9301] [depth= 1] . ( 500 sec) [ -35975.2493] [ 9298] [depth= 1] . ( 500 sec) [ -35968.7763] [ 9315] [depth= 1] . ( 500 sec) [ -35938.7796] [ 9298] [depth= 1] . ( 500 sec) [ -35887.6023] [ 9304] [depth= 2] . ( 501 sec) [ -35884.2680] [ 9303] [depth= 1] . ( 501 sec) [ -35880.5717] [ 9297] [depth= 1] . ( 501 sec) [ -35875.1233] [ 9303] [depth= 1] . ( 501 sec) [ -35874.6465] [ 9305] [depth= 1] . ( 501 sec) [ -35864.8674] [ 9297] [depth= 1] . ( 502 sec) [ -35863.5423] [ 9306] [depth= 1] . ( 502 sec) [ -35858.6607] [ 9306] [depth= 1] . ( 502 sec) [ -35852.2611] [ 9306] [depth= 1] . ( 502 sec) [ -35852.0001] [ 9315] [depth= 2] . ( 502 sec) [ -35846.9135] [ 9311] [depth= 1] . ( 502 sec) [ -35829.6825] [ 9315] [depth= 3] . ( 503 sec) [ -35827.8920] [ 9310] [depth= 1] . ( 503 sec) [ -35827.7338] [ 9321] [depth= 1] . ( 503 sec) [ -35824.8258] [ 9325] [depth= 3] . ( 504 sec) [ -35819.8487] [ 9325] [depth= 1] . ( 504 sec) [ -35815.7843] [ 9342] [depth= 2] . ( 504 sec) [ -35775.2913] [ 9308] [depth= 2] . ( 504 sec) [ -35760.4541] [ 9306] [depth= 1] . ( 504 sec) [ -35760.0837] [ 9308] [depth= 1] . ( 504 sec) [ -35751.5615] [ 9293] [depth= 1] . ( 504 sec) [ -35751.2427] [ 9297] [depth= 1] . ( 505 sec) [ -35710.4660] [ 9305] [depth= 2] . ( 505 sec) [ -35689.9691] [ 9317] [depth= 1] . ( 505 sec) [ -35688.5777] [ 9305] [depth= 1] . ( 505 sec) [ -35682.1110] [ 9313] [depth= 1] . ( 505 sec) [ -35656.4096] [ 9305] [depth= 1] . ( 505 sec) [ -35655.5026] [ 9312] [depth= 1] . ( 506 sec) [ -35631.6799] [ 9305] [depth= 1] . ( 507 sec) [ -35625.7289] [ 9308] [depth= 2] . ( 507 sec) [ -35625.0817] [ 9310] [depth= 1] . ( 507 sec) [ -35607.5665] [ 9307] [depth= 2] . ( 507 sec) [ -35605.1079] [ 9300] [depth= 1] . ( 507 sec) [ -35599.8424] [ 9297] [depth= 1] . ( 508 sec) [ -35592.2210] [ 9296] [depth= 1] . ( 508 sec) [ -35591.1458] [ 9293] [depth= 4] . ( 508 sec) [ -35585.1968] [ 9298] [depth= 1] . ( 508 sec) [ -35574.7206] [ 9293] [depth= 1] . ( 509 sec) [ -35574.2143] [ 9294] [depth= 1] . ( 509 sec) [ -35572.8797] [ 9293] [depth= 1] . ( 509 sec) [ -35562.7145] [ 9292] [depth= 1] . ( 509 sec) [ -35540.5258] [ 9293] [depth= 4] . ( 510 sec) [ -35539.9085] [ 9296] [depth= 1] . ( 510 sec) [ -35538.6142] [ 9293] [depth= 1] . ( 510 sec) [ -35536.1295] [ 9297] [depth= 1] . ( 510 sec) [ -35535.8295] [ 9293] [depth= 1] . ( 511 sec) [ -35307.7251] [Branch lengths ] . ( 516 sec) [ -35261.3733] [GTR parameters ] . ( 516 sec) [ -35253.2992] [Alpha ][ 0.446766] . ( 518 sec) [ -35252.6688] [ 9291] [depth= 1] . ( 519 sec) [ -35250.7935] [ 9286] [depth= 1] . ( 520 sec) [ -35250.2314] [ 9301] [depth= 1] . ( 522 sec) [ -35248.4647] [ 9297] [depth= 2] . ( 524 sec) [ -35246.5006] [ 9294] [depth= 1] . ( 526 sec) [ -35244.2970] [ 9296] [depth= 1] . ( 529 sec) [ -35241.2339] [ 9300] [depth= 2] . ( 533 sec) [ -35190.3187] [Branch lengths ] . ( 536 sec) [ -35185.9729] [GTR parameters ] . ( 537 sec) [ -35185.8197] [Alpha ][ 0.453722] . ( 555 sec) [ -35164.7563] [Branch lengths ] . ( 609 sec) [ -35164.6971] [ 9316] [depth= 2] . ( 644 sec) [ -35153.5642] [Branch lengths ] . ( 648 sec) [ -35148.5085] [GTR parameters ] . ( 648 sec) [ -35148.5075] [Alpha ][ 0.454222] . ( 669 sec) [ -35147.8960] [ 9320] [depth= 2] . ( 687 sec) [ -35146.8259] [ 9313] [depth= 1] . ( 692 sec) [ -35146.5948] [ 9312] [depth= 1] . ( 735 sec) [ -35129.9511] [Branch lengths ] . ( 737 sec) [ -35129.0559] [GTR parameters ] . ( 738 sec) [ -35128.9617] [Alpha ][ 0.449161] . ( 826 sec) [ -35120.6288] [Branch lengths ] . ( 826 sec) [ -35120.6288] [Topology ] . ( 828 sec) [ -35118.3724] [Topology ] . ( 830 sec) [ -35117.2532] [Topology ] . ( 833 sec) [ -35116.4904] [Topology ] . ( 835 sec) [ -35115.9462] [Topology ] . ( 837 sec) [ -35115.5520] [Topology ] . ( 839 sec) [ -35115.2638] [Topology ] . ( 841 sec) [ -35113.4848] [GTR parameters ] . ( 842 sec) [ -35112.9793] [Alpha ][ 0.438143] . ( 842 sec) [ -35112.9793] [Topology ] . ( 844 sec) [ -35112.1231] [Topology ] . ( 847 sec) [ -35111.5575] [Topology ] . ( 849 sec) [ -35111.1487] [Topology ] . ( 851 sec) [ -35110.8490] [Topology ] . ( 853 sec) [ -35110.3984] [Topology ] . ( 856 sec) [ -35109.6908] [Topology ] . ( 858 sec) [ -35109.3750] [Topology ] . ( 860 sec) [ -35109.1688] [Topology ] . ( 863 sec) [ -35109.0240] [Topology ] . ( 869 sec) [ -35108.1575] [GTR parameters ] . ( 869 sec) [ -35107.7963] [Alpha ][ 0.429303] . ( 869 sec) [ -35107.7963] [Topology ] . ( 871 sec) [ -35107.4307] [Topology ] . ( 874 sec) [ -35107.1969] [Topology ] . ( 876 sec) [ -35107.0320] [Topology ] . ( 878 sec) [ -35106.9141] [Topology ] . ( 880 sec) [ -35106.8300] [Topology ] . ( 883 sec) [ -35106.7699] [Topology ] . ( 886 sec) [ -35106.6321] [GTR parameters ] . ( 886 sec) [ -35106.5436] [Alpha ][ 0.425027] . ( 886 sec) [ -35106.5436] [Topology ] . ( 888 sec) [ -35106.4210] [Topology ] . ( 891 sec) [ -35106.3406] [Topology ] . ( 893 sec) [ -35106.2841] [Topology ] . ( 895 sec) [ -35106.2441] [Topology ] . ( 898 sec) [ -35106.2158] [Topology ] . ( 900 sec) [ -35106.1958] [Topology ] . ( 902 sec) [ -35106.1554] [GTR parameters ] . ( 902 sec) [ -35106.1236] [Alpha ][ 0.422499] . ( 902 sec) [ -35106.1236] [Topology ] . ( 904 sec) [ -35106.0824] [Topology ] . ( 907 sec) [ -35106.0556] [Topology ] . ( 909 sec) [ -35106.0370] [Topology ] . ( 911 sec) [ -35106.0238] [Topology ] . ( 913 sec) [ -35106.0146] [Topology ] . ( 916 sec) [ -35106.0081] [Topology ] . ( 917 sec) [ -35105.9977] [GTR parameters ] . ( 917 sec) [ -35105.9870] [Alpha ][ 0.421041] . ( 917 sec) [ -35105.9870] [Topology ] . ( 920 sec) [ -35105.9749] [Topology ] . ( 922 sec) [ -35105.9669] [Topology ] . ( 924 sec) [ -35105.9614] [Topology ] . ( 927 sec) [ -35105.9576] [Topology ] . ( 929 sec) [ -35105.9549] [Topology ] . ( 931 sec) [ -35105.9530] [Topology ] . ( 933 sec) [ -35105.9485] [GTR parameters ] . ( 933 sec) [ -35105.9451] [Alpha ][ 0.420199] . ( 934 sec) [ -35105.9451] [Topology ] . ( 936 sec) [ -35105.9408] [Topology ] . ( 938 sec) [ -35105.9381] [Topology ] . ( 940 sec) [ -35105.9362] [Topology ] . ( 943 sec) [ -35105.9349] [Topology ] . ( 945 sec) [ -35105.9339] [Topology ] . ( 947 sec) [ -35105.9332] [GTR parameters ] . ( 947 sec) [ -35105.9325] [Alpha ][ 0.419779] . ( 947 sec) [ -35105.9325] [Topology ] . ( 949 sec) [ -35105.9311] [Topology ] . ( 952 sec) [ -35105.9303] [Topology ] . ( 953 sec) [ -35105.9299] [GTR parameters ] . ( 953 sec) [ -35105.9299] [Alpha ][ 0.419779] . ( 953 sec) [ -35105.9299] [Topology ] . ( 955 sec) [ -35105.9292] [Topology ] . ( 956 sec) [ -35105.9292] [GTR parameters ] . ( 956 sec) [ -35105.9292] [Alpha ][ 0.419779] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -35124.620116 . Log likelihood obtained after SPR moves : -35105.929217 . Log likelihood of the current tree: -35105.929217. . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Best log likelihood : -35105.928538 . Time used 0h16m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3630.51user 0.00system 1:00:47elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps