.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2786_104x1051_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 717 patterns found. (out of a total of 1051 sites) . 402 sites without polymorphism (38.25%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -37041.6374] [GTR parameters ] . ( 6 sec) [ -36238.9689] [Alpha ][ 0.500960] . ( 7 sec) [ -35907.5013] [ 6893] [depth= 13] . ( 7 sec) [ -35653.0075] [ 6837] [depth= 11] . ( 7 sec) [ -35634.3668] [ 6834] [depth= 2] . ( 7 sec) [ -35607.1396] [ 6820] [depth= 1] . ( 8 sec) [ -35572.9418] [ 6819] [depth= 1] . ( 8 sec) [ -35071.5078] [ 6819] [depth= 5] . ( 8 sec) [ -34441.1917] [ 6799] [depth= 3] . ( 8 sec) [ -34264.6313] [ 6743] [depth= 5] . ( 8 sec) [ -34238.9700] [ 6726] [depth= 5] . ( 8 sec) [ -34203.6194] [ 6721] [depth= 2] . ( 8 sec) [ -33822.1595] [ 6721] [depth= 2] . ( 9 sec) [ -33770.7573] [ 6704] [depth= 3] . ( 9 sec) [ -33755.6366] [ 6702] [depth= 5] . ( 9 sec) [ -33683.9538] [ 6682] [depth= 5] . ( 9 sec) [ -33589.0866] [ 6670] [depth= 10] . ( 9 sec) [ -33531.7161] [ 6669] [depth= 21] . ( 9 sec) [ -33518.3732] [ 6663] [depth= 7] . ( 10 sec) [ -33516.6929] [ 6664] [depth= 1] . ( 10 sec) [ -33406.6631] [ 6633] [depth= 18] . ( 10 sec) [ -33406.0078] [ 6633] [depth= 1] . ( 10 sec) [ -33278.2317] [ 6617] [depth= 10] . ( 10 sec) [ -33210.1757] [ 6592] [depth= 16] . ( 11 sec) [ -33089.9908] [ 6582] [depth= 1] . ( 11 sec) [ -32936.3274] [ 6561] [depth= 19] . ( 11 sec) [ -32523.3758] [ 6453] [depth= 17] . ( 11 sec) [ -32496.4181] [ 6439] [depth= 1] . ( 11 sec) [ -32295.3562] [ 6371] [depth= 11] . ( 12 sec) [ -32074.0633] [ 6342] [depth= 2] . ( 12 sec) [ -32007.4977] [ 6345] [depth= 1] . ( 12 sec) [ -31358.4577] [ 6250] [depth= 2] . ( 12 sec) [ -30616.0374] [ 6193] [depth= 18] . ( 12 sec) [ -30172.1353] [ 6066] [depth= 8] . ( 12 sec) [ -29881.3829] [ 6047] [depth= 1] . ( 13 sec) [ -29869.8925] [ 6041] [depth= 5] . ( 13 sec) [ -29854.3397] [ 6039] [depth= 1] . ( 13 sec) [ -29804.2243] [ 6025] [depth= 8] . ( 13 sec) [ -29796.5158] [ 6025] [depth= 3] . ( 13 sec) [ -29763.7622] [ 6025] [depth= 3] . ( 13 sec) [ -29746.6102] [ 6024] [depth= 2] . ( 14 sec) [ -29685.0595] [ 6005] [depth= 3] . ( 14 sec) [ -29651.9385] [ 5999] [depth= 12] . ( 14 sec) [ -29591.8383] [ 5999] [depth= 8] . ( 14 sec) [ -29463.8300] [ 5984] [depth= 7] . ( 14 sec) [ -29323.0504] [ 5956] [depth= 9] . ( 14 sec) [ -29272.4456] [ 5939] [depth= 2] . ( 15 sec) [ -29264.2526] [ 5938] [depth= 11] . ( 15 sec) [ -29235.0811] [ 5939] [depth= 16] . ( 15 sec) [ -29042.8509] [ 5903] [depth= 15] . ( 15 sec) [ -28891.6337] [ 5879] [depth= 16] . ( 15 sec) [ -28891.0343] [ 5878] [depth= 1] . ( 16 sec) [ -28675.3517] [ 5849] [depth= 1] . ( 16 sec) [ -28520.7012] [ 5817] [depth= 7] . ( 16 sec) [ -28471.0468] [ 5817] [depth= 6] . ( 16 sec) [ -28456.2974] [ 5825] [depth= 1] . ( 16 sec) [ -28436.1833] [ 5817] [depth= 1] . ( 17 sec) [ -28301.8038] [ 5764] [depth= 9] . ( 17 sec) [ -28162.2307] [ 5733] [depth= 16] . ( 17 sec) [ -27896.2300] [ 5678] [depth= 19] . ( 17 sec) [ -27503.4403] [ 5610] [depth= 1] . ( 17 sec) [ -27302.7757] [ 5545] [depth= 18] . ( 17 sec) [ -26770.7535] [ 5485] [depth= 10] . ( 18 sec) [ -26739.3560] [ 5484] [depth= 8] . ( 18 sec) [ -26366.0562] [ 5484] [depth= 1] . ( 18 sec) [ -26222.5156] [ 5369] [depth= 12] . ( 18 sec) [ -26135.1203] [ 5352] [depth= 1] . ( 19 sec) [ -26042.1897] [ 5333] [depth= 11] . ( 19 sec) [ -26026.8220] [ 5327] [depth= 12] . ( 19 sec) [ -25984.2112] [ 5320] [depth= 13] . ( 19 sec) [ -25945.9019] [ 5314] [depth= 11] . ( 19 sec) [ -25829.7902] [ 5294] [depth= 5] . ( 20 sec) [ -25753.7322] [ 5286] [depth= 2] . ( 20 sec) [ -25649.0135] [ 5281] [depth= 11] . ( 20 sec) [ -25514.8213] [ 5273] [depth= 6] . ( 20 sec) [ -25502.3071] [ 5269] [depth= 1] . ( 20 sec) [ -25463.2541] [ 5267] [depth= 2] . ( 20 sec) [ -25452.9762] [ 5260] [depth= 7] . ( 21 sec) [ -25436.3704] [ 5260] [depth= 7] . ( 21 sec) [ -25423.1947] [ 5256] [depth= 6] . ( 21 sec) [ -25388.9433] [ 5258] [depth= 1] . ( 21 sec) [ -25231.0307] [ 5205] [depth= 15] . ( 21 sec) [ -25193.2056] [ 5249] [depth= 1] . ( 21 sec) [ -25075.1093] [ 5220] [depth= 8] . ( 22 sec) [ -24916.1033] [ 5178] [depth= 16] . ( 22 sec) [ -24875.8504] [ 5179] [depth= 4] . ( 22 sec) [ -24811.8163] [ 5135] [depth= 1] . ( 22 sec) [ -24767.2141] [ 5125] [depth= 13] . ( 22 sec) [ -24761.8495] [ 5123] [depth= 1] . ( 23 sec) [ -24732.9529] [ 5121] [depth= 1] . ( 23 sec) [ -24720.1073] [ 5124] [depth= 6] . ( 23 sec) [ -24693.3185] [ 5120] [depth= 3] . ( 23 sec) [ -24567.5835] [ 5086] [depth= 2] . ( 23 sec) [ -24511.7049] [ 5064] [depth= 9] . ( 23 sec) [ -24472.0107] [ 5060] [depth= 7] . ( 24 sec) [ -24416.2051] [ 5047] [depth= 6] . ( 24 sec) [ -24411.1280] [ 5039] [depth= 3] . ( 24 sec) [ -24367.8703] [ 5026] [depth= 1] . ( 24 sec) [ -24323.6985] [ 5023] [depth= 9] . ( 25 sec) [ -24292.6296] [ 5024] [depth= 5] . ( 25 sec) [ -24264.1367] [ 5015] [depth= 14] . ( 25 sec) [ -24210.6098] [ 5002] [depth= 5] . ( 25 sec) [ -24154.1345] [ 4995] [depth= 13] . ( 25 sec) [ -24133.0994] [ 4994] [depth= 2] . ( 26 sec) [ -24131.4515] [ 4996] [depth= 16] . ( 26 sec) [ -24122.8140] [ 4995] [depth= 10] . ( 26 sec) [ -24106.4244] [ 4997] [depth= 17] . ( 26 sec) [ -24106.3520] [ 4998] [depth= 1] . ( 26 sec) [ -24090.1798] [ 4999] [depth= 6] . ( 27 sec) [ -24055.4345] [ 4994] [depth= 2] . ( 27 sec) [ -24044.7091] [ 4991] [depth= 9] . ( 27 sec) [ -24023.0322] [ 4990] [depth= 2] . ( 27 sec) [ -23927.6813] [ 4964] [depth= 5] . ( 27 sec) [ -23778.6936] [ 4942] [depth= 5] . ( 27 sec) [ -23439.1730] [ 4931] [depth= 4] . ( 28 sec) [ -23351.7349] [ 4961] [depth= 1] . ( 28 sec) [ -22982.0765] [ 4937] [depth= 13] . ( 28 sec) [ -22944.9361] [ 4928] [depth= 1] . ( 28 sec) [ -22798.5578] [ 4797] [depth= 4] . ( 28 sec) [ -22745.4494] [ 4774] [depth= 5] . ( 29 sec) [ -22740.1363] [ 4759] [depth= 1] . ( 29 sec) [ -22478.3013] [ 4648] [depth= 11] . ( 29 sec) [ -22465.5902] [ 4641] [depth= 3] . ( 29 sec) [ -22464.9678] [ 4643] [depth= 1] . ( 29 sec) [ -22439.8824] [ 4637] [depth= 9] . ( 30 sec) [ -22424.9070] [ 4635] [depth= 2] . ( 30 sec) [ -22392.1055] [ 4626] [depth= 10] . ( 30 sec) [ -22359.4886] [ 4625] [depth= 1] . ( 30 sec) [ -21995.0931] [ 4595] [depth= 8] . ( 31 sec) [ -21982.1142] [ 4591] [depth= 14] . ( 31 sec) [ -21946.4170] [ 4586] [depth= 9] . ( 31 sec) [ -21912.5927] [ 4586] [depth= 2] . ( 31 sec) [ -21866.5494] [ 4571] [depth= 1] . ( 31 sec) [ -21764.5540] [ 4541] [depth= 8] . ( 32 sec) [ -21744.3657] [ 4521] [depth= 2] . ( 32 sec) [ -21717.4184] [ 4516] [depth= 12] . ( 32 sec) [ -21677.7200] [ 4507] [depth= 5] . ( 32 sec) [ -21529.9590] [ 4430] [depth= 5] . ( 32 sec) [ -21524.1751] [ 4429] [depth= 1] . ( 33 sec) [ -21486.0506] [ 4427] [depth= 6] . ( 33 sec) [ -21436.1049] [ 4422] [depth= 1] . ( 33 sec) [ -21375.4590] [ 4371] [depth= 10] . ( 34 sec) [ -21284.9505] [ 4333] [depth= 3] . ( 34 sec) [ -21159.3062] [ 4325] [depth= 10] . ( 34 sec) [ -21112.5453] [ 4313] [depth= 9] . ( 35 sec) [ -20940.4669] [ 4290] [depth= 3] . ( 35 sec) [ -20890.3566] [ 4290] [depth= 2] . ( 35 sec) [ -20877.6268] [ 4290] [depth= 1] . ( 36 sec) [ -20857.9241] [ 4290] [depth= 1] . ( 36 sec) [ -20856.0770] [ 4291] [depth= 2] . ( 36 sec) [ -20850.8646] [ 4289] [depth= 15] . ( 36 sec) [ -20815.4545] [ 4280] [depth= 8] . ( 36 sec) [ -20686.7852] [ 4276] [depth= 1] . ( 37 sec) [ -20407.3428] [ 4187] [depth= 6] . ( 37 sec) [ -20293.4579] [ 4158] [depth= 10] . ( 37 sec) [ -20271.6755] [ 4145] [depth= 1] . ( 38 sec) [ -20247.9496] [ 4144] [depth= 1] . ( 38 sec) [ -20242.8542] [ 4144] [depth= 2] . ( 38 sec) [ -20226.4404] [ 4144] [depth= 3] . ( 38 sec) [ -20215.3470] [ 4143] [depth= 3] . ( 39 sec) [ -20211.7922] [ 4140] [depth= 1] . ( 39 sec) [ -20136.7458] [ 4126] [depth= 2] . ( 39 sec) [ -20129.3329] [ 4127] [depth= 1] . ( 39 sec) [ -20047.9876] [ 4074] [depth= 9] . ( 39 sec) [ -20047.4701] [ 4075] [depth= 1] . ( 39 sec) [ -20016.6607] [ 4063] [depth= 2] . ( 40 sec) [ -19341.9043] [ 4063] [depth= 13] . ( 40 sec) [ -19340.1932] [ 4064] [depth= 1] . ( 40 sec) [ -19333.0514] [ 4042] [depth= 14] . ( 40 sec) [ -19274.1013] [ 4023] [depth= 10] . ( 40 sec) [ -19159.3231] [ 3908] [depth= 15] . ( 41 sec) [ -19158.8551] [ 3908] [depth= 1] . ( 41 sec) [ -19158.0200] [ 3909] [depth= 6] . ( 41 sec) [ -19133.3374] [ 3904] [depth= 2] . ( 41 sec) [ -19083.4901] [ 3897] [depth= 2] . ( 42 sec) [ -19058.1144] [ 3900] [depth= 4] . ( 42 sec) [ -18983.5920] [ 3877] [depth= 4] . ( 42 sec) [ -18983.3695] [ 3878] [depth= 1] . ( 42 sec) [ -18364.5658] [ 3796] [depth= 3] . ( 42 sec) [ -18349.2079] [ 3795] [depth= 1] . ( 43 sec) [ -18343.6568] [ 3794] [depth= 1] . ( 43 sec) [ -18329.0229] [ 3790] [depth= 1] . ( 43 sec) [ -18325.5588] [ 3791] [depth= 1] . ( 43 sec) [ -18235.0438] [ 3771] [depth= 5] . ( 43 sec) [ -18207.5091] [ 3765] [depth= 1] . ( 44 sec) [ -18207.2345] [ 3765] [depth= 1] . ( 44 sec) [ -18205.5503] [ 3765] [depth= 1] . ( 44 sec) [ -18068.8132] [ 3734] [depth= 5] . ( 44 sec) [ -18060.0799] [ 3730] [depth= 4] . ( 44 sec) [ -18050.7164] [ 3731] [depth= 1] . ( 45 sec) [ -17984.9254] [ 3710] [depth= 7] . ( 45 sec) [ -17984.0253] [ 3711] [depth= 1] . ( 45 sec) [ -17934.8415] [ 3713] [depth= 1] . ( 46 sec) [ -17934.8083] [ 3715] [depth= 1] . ( 46 sec) [ -17933.8512] [ 3714] [depth= 1] . ( 46 sec) [ -17931.8338] [ 3707] [depth= 7] . ( 46 sec) [ -17773.6053] [ 3735] [depth= 1] . ( 47 sec) [ -17711.1142] [ 3684] [depth= 6] . ( 47 sec) [ -17700.1796] [ 3678] [depth= 1] . ( 47 sec) [ -17697.4086] [ 3685] [depth= 1] . ( 47 sec) [ -17442.9353] [ 3631] [depth= 4] . ( 48 sec) [ -17441.8220] [ 3637] [depth= 1] . ( 48 sec) [ -17438.5130] [ 3637] [depth= 1] . ( 48 sec) [ -17422.9172] [ 3633] [depth= 2] . ( 48 sec) [ -17416.7725] [ 3632] [depth= 2] . ( 48 sec) [ -17298.0554] [ 3604] [depth= 15] . ( 49 sec) [ -17290.1592] [ 3602] [depth= 1] . ( 49 sec) [ -17289.9803] [ 3603] [depth= 1] . ( 49 sec) [ -17289.3744] [ 3603] [depth= 1] . ( 49 sec) [ -17287.6793] [ 3603] [depth= 1] . ( 49 sec) [ -17266.6991] [ 3600] [depth= 11] . ( 50 sec) [ -17194.7513] [ 3584] [depth= 1] . ( 50 sec) [ -17186.8584] [ 3580] [depth= 3] . ( 50 sec) [ -17182.9851] [ 3578] [depth= 1] . ( 50 sec) [ -17182.8273] [ 3578] [depth= 1] . ( 50 sec) [ -17166.8862] [ 3574] [depth= 1] . ( 51 sec) [ -17164.3320] [ 3574] [depth= 1] . ( 51 sec) [ -17098.7103] [ 3555] [depth= 4] . ( 51 sec) [ -17081.4870] [ 3559] [depth= 1] . ( 51 sec) [ -17013.9153] [ 3496] [depth= 5] . ( 52 sec) [ -17006.0104] [ 3498] [depth= 1] . ( 52 sec) [ -16975.4384] [ 3494] [depth= 8] . ( 52 sec) [ -16766.5821] [ 3488] [depth= 1] . ( 52 sec) [ -16692.1404] [ 3442] [depth= 3] . ( 52 sec) [ -16656.4475] [ 3396] [depth= 4] . ( 53 sec) [ -16631.1733] [ 3396] [depth= 7] . ( 53 sec) [ -16617.4167] [ 3388] [depth= 4] . ( 53 sec) [ -16604.8631] [ 3388] [depth= 3] . ( 53 sec) [ -16602.9737] [ 3393] [depth= 5] . ( 53 sec) [ -16600.2467] [ 3393] [depth= 2] . ( 53 sec) [ -16543.8186] [ 3375] [depth= 6] . ( 54 sec) [ -16512.7436] [ 3381] [depth= 1] . ( 54 sec) [ -16499.2808] [ 3379] [depth= 1] . ( 54 sec) [ -16496.2171] [ 3378] [depth= 1] . ( 54 sec) [ -16489.9129] [ 3371] [depth= 1] . ( 55 sec) [ -16489.6698] [ 3370] [depth= 1] . ( 55 sec) [ -16461.3894] [ 3365] [depth= 1] . ( 55 sec) [ -16460.3875] [ 3365] [depth= 1] . ( 57 sec) [ -16127.2831] [Branch lengths ] . ( 64 sec) [ -16086.8538] [GTR parameters ] . ( 65 sec) [ -16086.6166] [Alpha ][ 0.516875] . ( 66 sec) [ -16085.1203] [ 3363] [depth= 1] . ( 66 sec) [ -16072.4598] [ 3351] [depth= 2] . ( 66 sec) [ -16065.8114] [ 3346] [depth= 2] . ( 67 sec) [ -16064.9394] [ 3341] [depth= 1] . ( 67 sec) [ -16054.8167] [ 3334] [depth= 6] . ( 67 sec) [ -15972.1106] [ 3313] [depth= 1] . ( 67 sec) [ -15947.2248] [ 3306] [depth= 3] . ( 69 sec) [ -15940.8986] [ 3305] [depth= 1] . ( 70 sec) [ -15923.9223] [ 3292] [depth= 1] . ( 70 sec) [ -15917.8479] [ 3297] [depth= 1] . ( 70 sec) [ -15897.6315] [ 3294] [depth= 1] . ( 71 sec) [ -15895.6949] [ 3293] [depth= 1] . ( 71 sec) [ -15894.8885] [ 3293] [depth= 1] . ( 72 sec) [ -15889.7155] [ 3291] [depth= 1] . ( 72 sec) [ -15884.3849] [ 3290] [depth= 1] . ( 72 sec) [ -15875.9416] [ 3290] [depth= 1] . ( 72 sec) [ -15873.8830] [ 3287] [depth= 1] . ( 74 sec) [ -15870.4362] [ 3287] [depth= 1] . ( 75 sec) [ -15863.9746] [ 3285] [depth= 1] . ( 75 sec) [ -15863.1216] [ 3284] [depth= 1] . ( 75 sec) [ -15858.7549] [ 3282] [depth= 2] . ( 75 sec) [ -15858.7195] [ 3282] [depth= 1] . ( 76 sec) [ -15832.9470] [ 3283] [depth= 6] . ( 76 sec) [ -15832.5464] [ 3282] [depth= 3] . ( 77 sec) [ -15831.7646] [ 3282] [depth= 1] . ( 77 sec) [ -15831.3410] [ 3280] [depth= 1] . ( 78 sec) [ -15830.2842] [ 3280] [depth= 1] . ( 79 sec) [ -15821.8967] [ 3281] [depth= 1] . ( 80 sec) [ -15821.8775] [ 3281] [depth= 1] . ( 83 sec) [ -15817.6626] [ 3280] [depth= 1] . ( 83 sec) [ -15816.1284] [ 3282] [depth= 2] . ( 83 sec) [ -15815.2522] [ 3282] [depth= 1] . ( 83 sec) [ -15813.7616] [ 3281] [depth= 1] . ( 84 sec) [ -15813.2588] [ 3284] [depth= 1] . ( 86 sec) [ -15811.9586] [ 3282] [depth= 1] . ( 86 sec) [ -15811.5111] [ 3282] [depth= 1] . ( 87 sec) [ -15811.4143] [ 3282] [depth= 1] . ( 88 sec) [ -15810.5342] [ 3281] [depth= 1] . ( 88 sec) [ -15799.8684] [ 3280] [depth= 1] . ( 89 sec) [ -15799.2939] [ 3279] [depth= 1] . ( 89 sec) [ -15796.0706] [ 3277] [depth= 2] . ( 90 sec) [ -15795.6036] [ 3275] [depth= 1] . ( 90 sec) [ -15788.5190] [ 3258] [depth= 3] . ( 91 sec) [ -15759.1022] [ 3246] [depth= 1] . ( 92 sec) [ -15757.5780] [ 3246] [depth= 3] . ( 92 sec) [ -15756.8931] [ 3244] [depth= 1] . ( 92 sec) [ -15756.1413] [ 3246] [depth= 4] . ( 92 sec) [ -15747.2290] [ 3232] [depth= 2] . ( 92 sec) [ -15735.9451] [ 3226] [depth= 2] . ( 93 sec) [ -15735.6959] [ 3231] [depth= 1] . ( 93 sec) [ -15733.6186] [ 3233] [depth= 2] . ( 95 sec) [ -15728.6497] [ 3230] [depth= 1] . ( 96 sec) [ -15728.2220] [ 3230] [depth= 1] . ( 97 sec) [ -15727.9082] [ 3229] [depth= 3] . ( 98 sec) [ -15720.0373] [ 3219] [depth= 1] . ( 98 sec) [ -15720.0182] [ 3219] [depth= 1] . ( 99 sec) [ -15718.6271] [ 3218] [depth= 1] . ( 102 sec) [ -15715.2520] [ 3212] [depth= 1] . ( 103 sec) [ -15715.1445] [ 3212] [depth= 1] . ( 104 sec) [ -15713.0999] [ 3213] [depth= 1] . ( 106 sec) [ -15711.9659] [ 3210] [depth= 1] . ( 106 sec) [ -15711.8758] [ 3210] [depth= 1] . ( 106 sec) [ -15708.3978] [ 3208] [depth= 1] . ( 107 sec) [ -15707.8841] [ 3206] [depth= 1] . ( 107 sec) [ -15705.1627] [ 3207] [depth= 1] . ( 108 sec) [ -15704.7872] [ 3208] [depth= 2] . ( 109 sec) [ -15704.4101] [ 3208] [depth= 1] . ( 109 sec) [ -15704.3926] [ 3208] [depth= 1] . ( 110 sec) [ -15704.3405] [ 3207] [depth= 1] . ( 110 sec) [ -15704.1534] [ 3207] [depth= 1] . ( 110 sec) [ -15702.6115] [ 3206] [depth= 2] . ( 112 sec) [ -15702.3388] [ 3205] [depth= 2] . ( 113 sec) [ -15701.5953] [ 3204] [depth= 1] . ( 113 sec) [ -15700.7063] [ 3205] [depth= 1] . ( 116 sec) [ -15669.7080] [Branch lengths ] . ( 121 sec) [ -15669.3987] [GTR parameters ] . ( 121 sec) [ -15668.7206] [Alpha ][ 0.545811] . ( 128 sec) [ -15668.1465] [ 3205] [depth= 2] . ( 131 sec) [ -15668.1361] [ 3205] [depth= 1] . ( 133 sec) [ -15666.2207] [ 3204] [depth= 1] . ( 133 sec) [ -15665.0471] [ 3203] [depth= 2] . ( 134 sec) [ -15663.7655] [ 3204] [depth= 1] . ( 141 sec) [ -15663.5765] [ 3205] [depth= 1] . ( 172 sec) [ -15663.5529] [ 3204] [depth= 1] . ( 178 sec) [ -15660.4521] [Branch lengths ] . ( 183 sec) [ -15660.4180] [GTR parameters ] . ( 183 sec) [ -15660.4143] [Alpha ][ 0.548026] . ( 240 sec) [ -15660.2152] [Branch lengths ] . ( 388 sec) [ -15660.1621] [Branch lengths ] . ( 389 sec) [ -15660.1621] [Topology ] . ( 392 sec) [ -15660.1476] [Topology ] . ( 396 sec) [ -15660.1387] [Topology ] . ( 399 sec) [ -15660.1316] [Topology ] . ( 402 sec) [ -15660.1259] [Topology ] . ( 406 sec) [ -15660.1211] [Topology ] . ( 409 sec) [ -15660.1171] [Topology ] . ( 413 sec) [ -15660.1122] [GTR parameters ] . ( 413 sec) [ -15660.1117] [Alpha ][ 0.548781] . ( 413 sec) [ -15660.1117] [Topology ] . ( 417 sec) [ -15660.1074] [Topology ] . ( 420 sec) [ -15660.1037] [Topology ] . ( 424 sec) [ -15660.1006] [Topology ] . ( 427 sec) [ -15660.0978] [Topology ] . ( 431 sec) [ -15660.0952] [Topology ] . ( 434 sec) [ -15660.0929] [Topology ] . ( 435 sec) [ -15660.0927] [GTR parameters ] . ( 436 sec) [ -15660.0927] [Alpha ][ 0.548781] . ( 436 sec) [ -15660.0927] [Topology ] . ( 439 sec) [ -15660.0905] [Topology ] . ( 443 sec) [ -15660.0884] [Topology ] . ( 446 sec) [ -15660.0864] [Topology ] . ( 450 sec) [ -15660.0845] [Topology ] . ( 453 sec) [ -15660.0827] [Topology ] . ( 457 sec) [ -15660.0810] [Topology ] . ( 458 sec) [ -15660.0809] [GTR parameters ] . ( 458 sec) [ -15660.0809] [Alpha ][ 0.548781] . ( 458 sec) [ -15660.0809] [Topology ] . ( 462 sec) [ -15660.0791] [Topology ] . ( 465 sec) [ -15660.0774] [Topology ] . ( 469 sec) [ -15660.0757] [Topology ] . ( 472 sec) [ -15660.0740] [Topology ] . ( 476 sec) [ -15660.0724] [Topology ] . ( 479 sec) [ -15660.0707] [Topology ] . ( 480 sec) [ -15660.0707] [GTR parameters ] . ( 480 sec) [ -15660.0707] [Alpha ][ 0.548781] . ( 480 sec) [ -15660.0707] [Topology ] . ( 483 sec) [ -15660.0691] [Topology ] . ( 487 sec) [ -15660.0675] [Topology ] . ( 490 sec) [ -15660.0659] [Topology ] . ( 494 sec) [ -15660.0642] [Topology ] . ( 497 sec) [ -15660.0626] [Topology ] . ( 501 sec) [ -15660.0610] [Topology ] . ( 502 sec) [ -15660.0610] [GTR parameters ] . ( 502 sec) [ -15660.0610] [Alpha ][ 0.548781] . ( 502 sec) [ -15660.0610] [Topology ] . ( 506 sec) [ -15660.0594] [Topology ] . ( 509 sec) [ -15660.0578] [Topology ] . ( 512 sec) [ -15660.0562] [Topology ] . ( 516 sec) [ -15660.0546] [Topology ] . ( 519 sec) [ -15660.0530] [Topology ] . ( 523 sec) [ -15660.0514] [Topology ] . ( 525 sec) [ -15660.0513] [GTR parameters ] . ( 525 sec) [ -15660.0513] [Alpha ][ 0.548781] . ( 525 sec) [ -15660.0513] [Topology ] . ( 528 sec) [ -15660.0497] [Topology ] . ( 532 sec) [ -15660.0480] [Topology ] . ( 535 sec) [ -15660.0463] [Topology ] . ( 539 sec) [ -15660.0446] [Topology ] . ( 542 sec) [ -15660.0429] [Topology ] . ( 546 sec) [ -15660.0412] [Topology ] . ( 546 sec) [ -15660.0412] [GTR parameters ] . ( 547 sec) [ -15660.0412] [Alpha ][ 0.548781] . ( 547 sec) [ -15660.0412] [Topology ] . ( 550 sec) [ -15660.0395] [Topology ] . ( 554 sec) [ -15660.0386] [Topology ] . ( 554 sec) [ -15660.0386] [GTR parameters ] . ( 555 sec) [ -15660.0386] [Alpha ][ 0.548781] . ( 555 sec) [ -15660.0386] [Topology ] . ( 558 sec) [ -15660.0383] [Topology ] . ( 559 sec) [ -15660.0383] [GTR parameters ] . ( 559 sec) [ -15660.0383] [Alpha ][ 0.548781] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15660.038278. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -36381.8790] [GTR parameters ] . ( 4 sec) [ -35609.4559] [Alpha ][ 0.500960] . ( 4 sec) [ -35313.4023] [ 6911] [depth= 13] . ( 4 sec) [ -34818.5443] [ 6859] [depth= 8] . ( 4 sec) [ -34692.8975] [ 6839] [depth= 12] . ( 5 sec) [ -34623.3136] [ 6828] [depth= 1] . ( 5 sec) [ -34418.8692] [ 6811] [depth= 19] . ( 5 sec) [ -34174.9266] [ 6799] [depth= 8] . ( 5 sec) [ -33934.4091] [ 6745] [depth= 1] . ( 5 sec) [ -33701.9843] [ 6734] [depth= 11] . ( 6 sec) [ -33298.8774] [ 6676] [depth= 1] . ( 6 sec) [ -33163.4804] [ 6662] [depth= 4] . ( 6 sec) [ -33015.4502] [ 6573] [depth= 1] . ( 6 sec) [ -32926.5347] [ 6566] [depth= 8] . ( 6 sec) [ -32901.0055] [ 6560] [depth= 1] . ( 6 sec) [ -32830.6161] [ 6549] [depth= 4] . ( 7 sec) [ -32763.1684] [ 6539] [depth= 6] . ( 7 sec) [ -32476.3785] [ 6536] [depth= 1] . ( 7 sec) [ -32378.7382] [ 6521] [depth= 5] . ( 7 sec) [ -32333.5683] [ 6514] [depth= 8] . ( 7 sec) [ -32265.6167] [ 6496] [depth= 8] . ( 7 sec) [ -32161.4723] [ 6467] [depth= 22] . ( 8 sec) [ -32110.5632] [ 6470] [depth= 1] . ( 8 sec) [ -32077.2046] [ 6460] [depth= 1] . ( 8 sec) [ -32057.3941] [ 6467] [depth= 2] . ( 8 sec) [ -31995.0982] [ 6457] [depth= 23] . ( 8 sec) [ -31940.7922] [ 6454] [depth= 1] . ( 9 sec) [ -31837.8089] [ 6413] [depth= 27] . ( 9 sec) [ -31187.9171] [ 6284] [depth= 13] . ( 9 sec) [ -31064.6975] [ 6249] [depth= 1] . ( 9 sec) [ -30951.7329] [ 6202] [depth= 4] . ( 9 sec) [ -30898.6461] [ 6201] [depth= 19] . ( 10 sec) [ -30469.1844] [ 6162] [depth= 19] . ( 10 sec) [ -30358.5719] [ 6160] [depth= 1] . ( 10 sec) [ -29934.1001] [ 6078] [depth= 18] . ( 10 sec) [ -29706.0061] [ 6060] [depth= 19] . ( 11 sec) [ -29492.8653] [ 6035] [depth= 21] . ( 11 sec) [ -29430.7021] [ 6013] [depth= 1] . ( 11 sec) [ -29415.0946] [ 6002] [depth= 8] . ( 11 sec) [ -29349.3849] [ 5974] [depth= 11] . ( 11 sec) [ -29243.2466] [ 5970] [depth= 1] . ( 12 sec) [ -28944.1864] [ 5925] [depth= 9] . ( 12 sec) [ -28913.4489] [ 5916] [depth= 2] . ( 12 sec) [ -28795.0741] [ 5883] [depth= 17] . ( 12 sec) [ -28781.5176] [ 5904] [depth= 1] . ( 12 sec) [ -28614.8375] [ 5868] [depth= 12] . ( 13 sec) [ -28284.6114] [ 5744] [depth= 1] . ( 13 sec) [ -28271.3791] [ 5742] [depth= 1] . ( 13 sec) [ -28233.8096] [ 5729] [depth= 1] . ( 13 sec) [ -28132.1745] [ 5722] [depth= 7] . ( 13 sec) [ -28128.0219] [ 5722] [depth= 1] . ( 14 sec) [ -28079.8352] [ 5707] [depth= 4] . ( 14 sec) [ -28074.2898] [ 5709] [depth= 2] . ( 14 sec) [ -28054.3397] [ 5707] [depth= 9] . ( 14 sec) [ -27479.4745] [ 5704] [depth= 3] . ( 14 sec) [ -27365.9493] [ 5701] [depth= 11] . ( 15 sec) [ -27353.1582] [ 5700] [depth= 1] . ( 15 sec) [ -27247.3349] [ 5697] [depth= 3] . ( 15 sec) [ -27218.1502] [ 5694] [depth= 2] . ( 15 sec) [ -27217.0911] [ 5690] [depth= 1] . ( 15 sec) [ -27161.8570] [ 5685] [depth= 5] . ( 15 sec) [ -27135.1745] [ 5670] [depth= 7] . ( 16 sec) [ -27132.1454] [ 5671] [depth= 1] . ( 16 sec) [ -27038.6089] [ 5644] [depth= 1] . ( 16 sec) [ -27002.9433] [ 5639] [depth= 7] . ( 16 sec) [ -26996.5664] [ 5640] [depth= 1] . ( 16 sec) [ -26645.0725] [ 5613] [depth= 8] . ( 17 sec) [ -26103.4352] [ 5503] [depth= 17] . ( 17 sec) [ -25792.6109] [ 5449] [depth= 1] . ( 17 sec) [ -25750.7462] [ 5441] [depth= 1] . ( 17 sec) [ -25740.6159] [ 5436] [depth= 5] . ( 18 sec) [ -25712.8675] [ 5428] [depth= 2] . ( 18 sec) [ -25661.7055] [ 5422] [depth= 8] . ( 18 sec) [ -25650.7819] [ 5424] [depth= 1] . ( 18 sec) [ -25570.4762] [ 5404] [depth= 2] . ( 18 sec) [ -25548.8710] [ 5397] [depth= 8] . ( 18 sec) [ -25524.4859] [ 5396] [depth= 1] . ( 19 sec) [ -25517.1121] [ 5395] [depth= 10] . ( 19 sec) [ -25509.8603] [ 5398] [depth= 2] . ( 19 sec) [ -25451.1476] [ 5388] [depth= 10] . ( 19 sec) [ -25332.6300] [ 5354] [depth= 8] . ( 19 sec) [ -25308.4928] [ 5347] [depth= 9] . ( 20 sec) [ -25269.3607] [ 5333] [depth= 11] . ( 20 sec) [ -25245.5237] [ 5325] [depth= 10] . ( 20 sec) [ -25205.8786] [ 5314] [depth= 9] . ( 20 sec) [ -25196.7425] [ 5312] [depth= 8] . ( 21 sec) [ -25194.1131] [ 5310] [depth= 10] . ( 21 sec) [ -25058.9570] [ 5269] [depth= 23] . ( 21 sec) [ -25038.2449] [ 5269] [depth= 13] . ( 21 sec) [ -24926.2899] [ 5267] [depth= 9] . ( 21 sec) [ -24919.3623] [ 5256] [depth= 5] . ( 21 sec) [ -24810.2846] [ 5232] [depth= 20] . ( 22 sec) [ -24753.3713] [ 5162] [depth= 4] . ( 22 sec) [ -24718.2599] [ 5149] [depth= 6] . ( 22 sec) [ -24655.9329] [ 5145] [depth= 2] . ( 23 sec) [ -24469.6827] [ 5080] [depth= 10] . ( 23 sec) [ -24388.0489] [ 5080] [depth= 7] . ( 23 sec) [ -24311.6434] [ 5068] [depth= 6] . ( 23 sec) [ -24291.9809] [ 5065] [depth= 5] . ( 23 sec) [ -24254.9946] [ 5064] [depth= 2] . ( 23 sec) [ -24226.0806] [ 5057] [depth= 6] . ( 23 sec) [ -24176.9260] [ 5058] [depth= 1] . ( 24 sec) [ -24128.9520] [ 5048] [depth= 1] . ( 24 sec) [ -24128.9187] [ 5049] [depth= 12] . ( 24 sec) [ -24090.9043] [ 5049] [depth= 13] . ( 24 sec) [ -23987.3485] [ 5044] [depth= 9] . ( 25 sec) [ -23903.6512] [ 5023] [depth= 21] . ( 25 sec) [ -23841.6071] [ 5016] [depth= 3] . ( 25 sec) [ -23813.2506] [ 5017] [depth= 1] . ( 25 sec) [ -23751.9479] [ 5010] [depth= 10] . ( 25 sec) [ -23747.0733] [ 5010] [depth= 1] . ( 26 sec) [ -23728.4860] [ 5015] [depth= 3] . ( 26 sec) [ -23727.7333] [ 5014] [depth= 1] . ( 26 sec) [ -23690.0871] [ 5010] [depth= 2] . ( 26 sec) [ -23688.9951] [ 5010] [depth= 1] . ( 26 sec) [ -23683.6125] [ 5011] [depth= 3] . ( 27 sec) [ -23678.0495] [ 5008] [depth= 1] . ( 27 sec) [ -23665.0026] [ 5001] [depth= 4] . ( 27 sec) [ -23661.5519] [ 5000] [depth= 1] . ( 27 sec) [ -23646.5531] [ 4993] [depth= 4] . ( 27 sec) [ -23634.2059] [ 4991] [depth= 17] . ( 27 sec) [ -23491.8668] [ 4959] [depth= 1] . ( 28 sec) [ -23046.9892] [ 4955] [depth= 1] . ( 28 sec) [ -23002.3978] [ 4952] [depth= 1] . ( 28 sec) [ -22998.5324] [ 4954] [depth= 17] . ( 28 sec) [ -22392.7947] [ 4823] [depth= 8] . ( 28 sec) [ -22362.5768] [ 4818] [depth= 14] . ( 28 sec) [ -22345.0313] [ 4814] [depth= 1] . ( 29 sec) [ -22230.6194] [ 4811] [depth= 15] . ( 29 sec) [ -22217.0609] [ 4810] [depth= 2] . ( 29 sec) [ -21988.9369] [ 4740] [depth= 2] . ( 30 sec) [ -21985.6815] [ 4740] [depth= 1] . ( 30 sec) [ -21961.9626] [ 4736] [depth= 1] . ( 30 sec) [ -21956.9106] [ 4736] [depth= 2] . ( 30 sec) [ -21948.4523] [ 4734] [depth= 3] . ( 30 sec) [ -21943.6722] [ 4734] [depth= 1] . ( 30 sec) [ -21932.7694] [ 4735] [depth= 1] . ( 31 sec) [ -21928.7139] [ 4734] [depth= 2] . ( 31 sec) [ -21772.9092] [ 4695] [depth= 7] . ( 31 sec) [ -21743.4618] [ 4684] [depth= 15] . ( 31 sec) [ -21740.6457] [ 4684] [depth= 1] . ( 31 sec) [ -21720.4023] [ 4681] [depth= 14] . ( 32 sec) [ -21715.0241] [ 4680] [depth= 2] . ( 32 sec) [ -21650.1775] [ 4684] [depth= 7] . ( 32 sec) [ -21602.8866] [ 4638] [depth= 1] . ( 32 sec) [ -21562.0508] [ 4622] [depth= 11] . ( 33 sec) [ -21557.3871] [ 4623] [depth= 2] . ( 33 sec) [ -21552.2074] [ 4623] [depth= 1] . ( 33 sec) [ -21533.3025] [ 4619] [depth= 1] . ( 33 sec) [ -21481.7756] [ 4604] [depth= 12] . ( 33 sec) [ -21462.3475] [ 4604] [depth= 1] . ( 34 sec) [ -21442.8225] [ 4604] [depth= 1] . ( 34 sec) [ -21438.9831] [ 4603] [depth= 4] . ( 34 sec) [ -21377.4020] [ 4579] [depth= 5] . ( 34 sec) [ -21363.0952] [ 4579] [depth= 1] . ( 35 sec) [ -21334.5945] [ 4572] [depth= 1] . ( 35 sec) [ -21328.9432] [ 4572] [depth= 19] . ( 35 sec) [ -21306.3166] [ 4565] [depth= 2] . ( 35 sec) [ -21251.1495] [ 4532] [depth= 1] . ( 35 sec) [ -21242.8076] [ 4531] [depth= 1] . ( 36 sec) [ -21230.8820] [ 4526] [depth= 6] . ( 36 sec) [ -21229.9643] [ 4522] [depth= 1] . ( 36 sec) [ -21229.7607] [ 4522] [depth= 1] . ( 37 sec) [ -21212.0671] [ 4516] [depth= 5] . ( 37 sec) [ -21154.6216] [ 4508] [depth= 16] . ( 37 sec) [ -21106.6218] [ 4487] [depth= 2] . ( 37 sec) [ -21056.3960] [ 4467] [depth= 1] . ( 38 sec) [ -21051.5505] [ 4471] [depth= 1] . ( 38 sec) [ -21051.4903] [ 4467] [depth= 2] . ( 38 sec) [ -21050.6494] [ 4470] [depth= 1] . ( 38 sec) [ -21050.5134] [ 4474] [depth= 1] . ( 38 sec) [ -21029.5438] [ 4459] [depth= 1] . ( 39 sec) [ -20940.6533] [ 4434] [depth= 3] . ( 39 sec) [ -20922.1950] [ 4441] [depth= 1] . ( 39 sec) [ -20782.7083] [ 4355] [depth= 1] . ( 39 sec) [ -20322.3140] [ 4338] [depth= 6] . ( 39 sec) [ -20185.1497] [ 4292] [depth= 9] . ( 40 sec) [ -20179.9850] [ 4292] [depth= 1] . ( 40 sec) [ -19451.2546] [ 4144] [depth= 2] . ( 40 sec) [ -19427.9028] [ 4142] [depth= 2] . ( 40 sec) [ -19408.6177] [ 4134] [depth= 1] . ( 41 sec) [ -19407.3621] [ 4097] [depth= 11] . ( 41 sec) [ -19310.4131] [ 4084] [depth= 4] . ( 41 sec) [ -19252.8605] [ 4082] [depth= 3] . ( 41 sec) [ -19226.8223] [ 4076] [depth= 3] . ( 41 sec) [ -19185.2546] [ 4068] [depth= 10] . ( 41 sec) [ -19174.9324] [ 4068] [depth= 1] . ( 42 sec) [ -19149.2846] [ 4073] [depth= 1] . ( 42 sec) [ -19138.9057] [ 4079] [depth= 1] . ( 42 sec) [ -19136.1247] [ 4062] [depth= 7] . ( 42 sec) [ -19074.6264] [ 4045] [depth= 2] . ( 42 sec) [ -18841.7587] [ 3956] [depth= 1] . ( 43 sec) [ -18805.1807] [ 3939] [depth= 14] . ( 43 sec) [ -18797.1358] [ 3943] [depth= 1] . ( 43 sec) [ -18735.1264] [ 3900] [depth= 3] . ( 43 sec) [ -18721.4099] [ 3888] [depth= 7] . ( 43 sec) [ -18655.0091] [ 3873] [depth= 14] . ( 44 sec) [ -18594.9819] [ 3857] [depth= 2] . ( 44 sec) [ -18581.1556] [ 3854] [depth= 1] . ( 44 sec) [ -18580.4654] [ 3854] [depth= 2] . ( 45 sec) [ -18480.3986] [ 3815] [depth= 7] . ( 45 sec) [ -18470.4767] [ 3818] [depth= 1] . ( 45 sec) [ -18218.9908] [ 3770] [depth= 1] . ( 45 sec) [ -18215.0828] [ 3773] [depth= 1] . ( 46 sec) [ -18170.0871] [ 3768] [depth= 11] . ( 46 sec) [ -18104.7805] [ 3756] [depth= 21] . ( 46 sec) [ -17805.8125] [ 3708] [depth= 24] . ( 46 sec) [ -17804.6854] [ 3709] [depth= 1] . ( 46 sec) [ -17799.5817] [ 3708] [depth= 1] . ( 47 sec) [ -17778.8836] [ 3705] [depth= 6] . ( 47 sec) [ -17772.6354] [ 3710] [depth= 1] . ( 47 sec) [ -17721.8319] [ 3700] [depth= 2] . ( 47 sec) [ -17711.5648] [ 3697] [depth= 1] . ( 47 sec) [ -17693.7987] [ 3696] [depth= 1] . ( 48 sec) [ -17692.1330] [ 3695] [depth= 3] . ( 48 sec) [ -17684.2470] [ 3695] [depth= 1] . ( 48 sec) [ -17675.3904] [ 3693] [depth= 1] . ( 48 sec) [ -17673.5243] [ 3693] [depth= 1] . ( 49 sec) [ -17671.4092] [ 3694] [depth= 1] . ( 49 sec) [ -17640.9540] [ 3690] [depth= 3] . ( 49 sec) [ -17612.6034] [ 3683] [depth= 2] . ( 49 sec) [ -17533.8355] [ 3687] [depth= 1] . ( 50 sec) [ -17521.3114] [ 3681] [depth= 2] . ( 50 sec) [ -17521.1300] [ 3682] [depth= 1] . ( 50 sec) [ -17441.5642] [ 3644] [depth= 1] . ( 50 sec) [ -17322.7471] [ 3612] [depth= 10] . ( 51 sec) [ -17190.1898] [ 3593] [depth= 4] . ( 51 sec) [ -17184.1921] [ 3591] [depth= 1] . ( 51 sec) [ -16946.2822] [ 3547] [depth= 7] . ( 52 sec) [ -16916.4975] [ 3546] [depth= 1] . ( 52 sec) [ -16912.0276] [ 3545] [depth= 1] . ( 52 sec) [ -16737.5677] [ 3431] [depth= 4] . ( 53 sec) [ -16733.7210] [ 3437] [depth= 1] . ( 54 sec) [ -16202.7986] [Branch lengths ] . ( 63 sec) [ -16109.0970] [GTR parameters ] . ( 63 sec) [ -16108.9873] [Alpha ][ 0.511711] . ( 63 sec) [ -16086.3414] [ 3423] [depth= 2] . ( 63 sec) [ -16082.0551] [ 3423] [depth= 3] . ( 64 sec) [ -16078.8684] [ 3422] [depth= 1] . ( 64 sec) [ -16078.7032] [ 3420] [depth= 2] . ( 65 sec) [ -16078.1341] [ 3416] [depth= 1] . ( 65 sec) [ -16035.1632] [ 3383] [depth= 12] . ( 65 sec) [ -16001.1078] [ 3368] [depth= 3] . ( 65 sec) [ -15999.3842] [ 3368] [depth= 2] . ( 65 sec) [ -15988.6763] [ 3364] [depth= 5] . ( 66 sec) [ -15988.1775] [ 3362] [depth= 2] . ( 66 sec) [ -15986.9246] [ 3359] [depth= 1] . ( 66 sec) [ -15984.5071] [ 3356] [depth= 1] . ( 66 sec) [ -15958.9378] [ 3352] [depth= 2] . ( 66 sec) [ -15958.6894] [ 3351] [depth= 1] . ( 67 sec) [ -15916.1220] [ 3300] [depth= 2] . ( 67 sec) [ -15914.9109] [ 3294] [depth= 1] . ( 67 sec) [ -15914.5505] [ 3295] [depth= 1] . ( 68 sec) [ -15908.2767] [ 3293] [depth= 1] . ( 70 sec) [ -15907.6081] [ 3294] [depth= 2] . ( 71 sec) [ -15907.1000] [ 3294] [depth= 1] . ( 71 sec) [ -15906.2730] [ 3295] [depth= 1] . ( 71 sec) [ -15904.4340] [ 3294] [depth= 1] . ( 72 sec) [ -15901.9531] [ 3286] [depth= 3] . ( 73 sec) [ -15872.5286] [ 3273] [depth= 7] . ( 74 sec) [ -15872.1702] [ 3273] [depth= 2] . ( 74 sec) [ -15830.7811] [ 3233] [depth= 5] . ( 76 sec) [ -15830.7104] [ 3233] [depth= 1] . ( 76 sec) [ -15830.5454] [ 3233] [depth= 1] . ( 77 sec) [ -15829.4351] [ 3233] [depth= 3] . ( 78 sec) [ -15829.0957] [ 3232] [depth= 1] . ( 79 sec) [ -15829.0626] [ 3232] [depth= 1] . ( 80 sec) [ -15819.8238] [ 3228] [depth= 7] . ( 80 sec) [ -15819.7852] [ 3228] [depth= 1] . ( 82 sec) [ -15803.9840] [ 3226] [depth= 3] . ( 83 sec) [ -15803.9415] [ 3226] [depth= 1] . ( 84 sec) [ -15803.8544] [ 3224] [depth= 1] . ( 84 sec) [ -15776.9128] [ 3218] [depth= 1] . ( 86 sec) [ -15775.7163] [ 3217] [depth= 3] . ( 86 sec) [ -15775.6628] [ 3217] [depth= 5] . ( 87 sec) [ -15774.3294] [ 3217] [depth= 1] . ( 89 sec) [ -15773.6165] [ 3216] [depth= 2] . ( 91 sec) [ -15773.4428] [ 3215] [depth= 1] . ( 91 sec) [ -15772.7604] [ 3220] [depth= 1] . ( 92 sec) [ -15772.1557] [ 3221] [depth= 1] . ( 93 sec) [ -15771.7849] [ 3219] [depth= 1] . ( 93 sec) [ -15771.7521] [ 3220] [depth= 1] . ( 93 sec) [ -15764.4628] [ 3218] [depth= 1] . ( 95 sec) [ -15763.4771] [ 3217] [depth= 1] . ( 96 sec) [ -15760.7534] [ 3215] [depth= 2] . ( 97 sec) [ -15753.9013] [ 3208] [depth= 1] . ( 97 sec) [ -15745.4049] [ 3206] [depth= 1] . ( 98 sec) [ -15743.6649] [ 3208] [depth= 1] . ( 98 sec) [ -15743.2939] [ 3208] [depth= 1] . ( 99 sec) [ -15742.2203] [ 3209] [depth= 2] . ( 101 sec) [ -15741.4463] [ 3209] [depth= 1] . ( 102 sec) [ -15738.6039] [ 3208] [depth= 1] . ( 102 sec) [ -15737.3463] [ 3208] [depth= 2] . ( 103 sec) [ -15735.6990] [ 3207] [depth= 1] . ( 104 sec) [ -15735.2483] [ 3206] [depth= 1] . ( 108 sec) [ -15686.8097] [Branch lengths ] . ( 116 sec) [ -15684.9565] [GTR parameters ] . ( 116 sec) [ -15684.4389] [Alpha ][ 0.536625] . ( 120 sec) [ -15684.1842] [ 3206] [depth= 1] . ( 122 sec) [ -15683.6874] [ 3205] [depth= 1] . ( 124 sec) [ -15682.4678] [ 3203] [depth= 1] . ( 126 sec) [ -15682.1430] [ 3203] [depth= 1] . ( 128 sec) [ -15680.1127] [ 3203] [depth= 1] . ( 130 sec) [ -15679.7633] [ 3203] [depth= 1] . ( 131 sec) [ -15679.5951] [ 3202] [depth= 1] . ( 131 sec) [ -15678.9856] [ 3202] [depth= 1] . ( 139 sec) [ -15678.8991] [ 3202] [depth= 2] . ( 144 sec) [ -15678.2403] [ 3201] [depth= 1] . ( 158 sec) [ -15677.0743] [ 3200] [depth= 1] . ( 170 sec) [ -15677.0139] [ 3199] [depth= 1] . ( 170 sec) [ -15676.3284] [ 3200] [depth= 1] . ( 175 sec) [ -15668.7087] [Branch lengths ] . ( 181 sec) [ -15668.5456] [GTR parameters ] . ( 181 sec) [ -15668.5201] [Alpha ][ 0.542415] . ( 193 sec) [ -15668.4012] [ 3200] [depth= 3] . ( 193 sec) [ -15667.7583] [ 3201] [depth= 1] . ( 199 sec) [ -15667.2475] [ 3200] [depth= 2] . ( 199 sec) [ -15666.8599] [ 3200] [depth= 1] . ( 202 sec) [ -15665.9789] [ 3200] [depth= 1] . ( 202 sec) [ -15665.8598] [ 3200] [depth= 1] . ( 203 sec) [ -15665.7297] [ 3200] [depth= 2] . ( 205 sec) [ -15665.1789] [ 3200] [depth= 1] . ( 210 sec) [ -15664.7781] [ 3199] [depth= 1] . ( 240 sec) [ -15661.2556] [Branch lengths ] . ( 242 sec) [ -15661.2419] [GTR parameters ] . ( 243 sec) [ -15661.2399] [Alpha ][ 0.544020] . ( 297 sec) [ -15659.4520] [Branch lengths ] . ( 382 sec) [ -15659.4406] [ 3196] [depth= 1] . ( 449 sec) [ -15658.6546] [Branch lengths ] . ( 452 sec) [ -15658.6499] [GTR parameters ] . ( 453 sec) [ -15658.6483] [Alpha ][ 0.545460] . ( 453 sec) [ -15658.6483] [Topology ] . ( 456 sec) [ -15658.5921] [Topology ] . ( 460 sec) [ -15658.5762] [Topology ] . ( 463 sec) [ -15658.5689] [Topology ] . ( 467 sec) [ -15658.5647] [Topology ] . ( 470 sec) [ -15658.5619] [Topology ] . ( 474 sec) [ -15658.5597] [Topology ] . ( 475 sec) [ -15658.5597] [GTR parameters ] . ( 475 sec) [ -15658.5597] [Alpha ][ 0.546005] . ( 475 sec) [ -15658.5597] [Topology ] . ( 478 sec) [ -15658.5577] [Topology ] . ( 482 sec) [ -15658.5560] [Topology ] . ( 485 sec) [ -15658.5543] [Topology ] . ( 489 sec) [ -15658.5526] [Topology ] . ( 492 sec) [ -15658.5510] [Topology ] . ( 496 sec) [ -15658.5493] [Topology ] . ( 497 sec) [ -15658.5492] [GTR parameters ] . ( 497 sec) [ -15658.5492] [Alpha ][ 0.546005] . ( 497 sec) [ -15658.5492] [Topology ] . ( 501 sec) [ -15658.5475] [Topology ] . ( 504 sec) [ -15658.5461] [Topology ] . ( 508 sec) [ -15658.5453] [Topology ] . ( 509 sec) [ -15658.5453] [GTR parameters ] . ( 509 sec) [ -15658.5453] [Alpha ][ 0.546005] . ( 509 sec) [ -15658.5453] [Topology ] . ( 512 sec) [ -15658.5450] [Topology ] . ( 513 sec) [ -15658.5450] [GTR parameters ] . ( 514 sec) [ -15658.5450] [Alpha ][ 0.546005] . Checking for NNIs, optimizing five branches... . ( 539 sec) [ -15658.5447] [Topology ] . Checking for NNIs, optimizing five branches... . ( 564 sec) [ -15658.5351] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15658.535132. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -36918.9442] [GTR parameters ] . ( 8 sec) [ -36109.5979] [Alpha ][ 0.500960] . ( 8 sec) [ -35913.5975] [ 7095] [depth= 12] . ( 9 sec) [ -35543.5311] [ 7040] [depth= 11] . ( 9 sec) [ -35493.1049] [ 7029] [depth= 2] . ( 9 sec) [ -35466.7813] [ 7022] [depth= 12] . ( 9 sec) [ -35427.7462] [ 7009] [depth= 3] . ( 9 sec) [ -35367.6256] [ 7005] [depth= 1] . ( 9 sec) [ -35333.0546] [ 6998] [depth= 4] . ( 9 sec) [ -35309.9492] [ 6991] [depth= 1] . ( 10 sec) [ -35230.3851] [ 6985] [depth= 15] . ( 10 sec) [ -35217.7103] [ 6978] [depth= 7] . ( 10 sec) [ -35206.6807] [ 6976] [depth= 5] . ( 10 sec) [ -34854.7030] [ 6963] [depth= 3] . ( 10 sec) [ -34781.0357] [ 6952] [depth= 11] . ( 10 sec) [ -34569.8263] [ 6935] [depth= 9] . ( 11 sec) [ -34379.3080] [ 6922] [depth= 1] . ( 11 sec) [ -34316.8630] [ 6897] [depth= 13] . ( 11 sec) [ -34273.8999] [ 6885] [depth= 2] . ( 11 sec) [ -34240.9955] [ 6884] [depth= 4] . ( 11 sec) [ -34122.9534] [ 6871] [depth= 11] . ( 11 sec) [ -33751.7837] [ 6859] [depth= 1] . ( 12 sec) [ -33612.4318] [ 6831] [depth= 18] . ( 12 sec) [ -33502.6847] [ 6806] [depth= 6] . ( 12 sec) [ -33409.6841] [ 6797] [depth= 19] . ( 12 sec) [ -33299.8225] [ 6769] [depth= 9] . ( 12 sec) [ -33266.6594] [ 6752] [depth= 5] . ( 13 sec) [ -32755.8080] [ 6743] [depth= 10] . ( 13 sec) [ -32721.0565] [ 6733] [depth= 17] . ( 13 sec) [ -32648.9163] [ 6730] [depth= 25] . ( 13 sec) [ -32347.8341] [ 6655] [depth= 14] . ( 13 sec) [ -32178.1453] [ 6623] [depth= 7] . ( 13 sec) [ -32068.4062] [ 6610] [depth= 4] . ( 14 sec) [ -32056.4951] [ 6609] [depth= 1] . ( 14 sec) [ -31472.2483] [ 6508] [depth= 11] . ( 14 sec) [ -31147.2358] [ 6444] [depth= 13] . ( 14 sec) [ -30499.9416] [ 6292] [depth= 18] . ( 14 sec) [ -30331.6258] [ 6377] [depth= 4] . ( 15 sec) [ -29902.4020] [ 6280] [depth= 17] . ( 15 sec) [ -29898.1945] [ 6281] [depth= 2] . ( 15 sec) [ -29881.5392] [ 6285] [depth= 5] . ( 15 sec) [ -29448.4945] [ 6237] [depth= 9] . ( 15 sec) [ -29285.0581] [ 6248] [depth= 1] . ( 15 sec) [ -28828.3656] [ 6222] [depth= 20] . ( 16 sec) [ -28421.9856] [ 6123] [depth= 1] . ( 16 sec) [ -28308.1680] [ 6103] [depth= 7] . ( 16 sec) [ -28291.3867] [ 6104] [depth= 1] . ( 16 sec) [ -28248.0408] [ 6067] [depth= 19] . ( 16 sec) [ -28209.4674] [ 6055] [depth= 3] . ( 16 sec) [ -28139.8830] [ 6036] [depth= 1] . ( 17 sec) [ -27879.1709] [ 5924] [depth= 1] . ( 17 sec) [ -27842.7586] [ 5915] [depth= 3] . ( 17 sec) [ -27632.7223] [ 5887] [depth= 18] . ( 17 sec) [ -27618.0006] [ 5889] [depth= 4] . ( 17 sec) [ -27616.5982] [ 5888] [depth= 1] . ( 18 sec) [ -27462.0387] [ 5850] [depth= 11] . ( 18 sec) [ -27164.1477] [ 5850] [depth= 1] . ( 18 sec) [ -27133.6889] [ 5846] [depth= 1] . ( 18 sec) [ -26691.2134] [ 5728] [depth= 19] . ( 18 sec) [ -26677.0328] [ 5727] [depth= 11] . ( 18 sec) [ -26670.1141] [ 5725] [depth= 1] . ( 19 sec) [ -26617.9537] [ 5706] [depth= 13] . ( 19 sec) [ -26525.2841] [ 5731] [depth= 12] . ( 19 sec) [ -26464.3147] [ 5712] [depth= 15] . ( 19 sec) [ -26062.6335] [ 5619] [depth= 9] . ( 19 sec) [ -25896.8656] [ 5592] [depth= 4] . ( 20 sec) [ -25762.7385] [ 5577] [depth= 17] . ( 20 sec) [ -25189.3623] [ 5445] [depth= 21] . ( 20 sec) [ -24848.8036] [ 5429] [depth= 4] . ( 20 sec) [ -24838.4912] [ 5431] [depth= 11] . ( 20 sec) [ -24756.7885] [ 5417] [depth= 11] . ( 20 sec) [ -24658.8250] [ 5391] [depth= 11] . ( 21 sec) [ -24343.2482] [ 5350] [depth= 25] . ( 21 sec) [ -24333.7576] [ 5351] [depth= 2] . ( 21 sec) [ -24291.8926] [ 5348] [depth= 8] . ( 21 sec) [ -24165.5118] [ 5317] [depth= 7] . ( 22 sec) [ -24164.8956] [ 5312] [depth= 5] . ( 22 sec) [ -24146.0415] [ 5309] [depth= 3] . ( 22 sec) [ -24052.8372] [ 5294] [depth= 15] . ( 22 sec) [ -23971.0938] [ 5275] [depth= 1] . ( 22 sec) [ -23928.3291] [ 5273] [depth= 8] . ( 22 sec) [ -23926.0270] [ 5275] [depth= 1] . ( 23 sec) [ -23923.3583] [ 5263] [depth= 16] . ( 23 sec) [ -23917.3644] [ 5263] [depth= 2] . ( 23 sec) [ -23588.0847] [ 5189] [depth= 9] . ( 23 sec) [ -23564.9747] [ 5190] [depth= 1] . ( 23 sec) [ -23458.6584] [ 5161] [depth= 24] . ( 24 sec) [ -23456.4360] [ 5155] [depth= 2] . ( 24 sec) [ -23345.0540] [ 5141] [depth= 1] . ( 24 sec) [ -23159.6480] [ 5123] [depth= 4] . ( 24 sec) [ -23154.3009] [ 5122] [depth= 1] . ( 24 sec) [ -23140.2631] [ 5126] [depth= 3] . ( 24 sec) [ -23131.0071] [ 5126] [depth= 1] . ( 25 sec) [ -23126.5379] [ 5129] [depth= 1] . ( 25 sec) [ -22714.1335] [ 5147] [depth= 18] . ( 25 sec) [ -22556.2815] [ 5109] [depth= 14] . ( 25 sec) [ -22494.2957] [ 5103] [depth= 7] . ( 25 sec) [ -22491.0318] [ 5102] [depth= 1] . ( 25 sec) [ -22373.1822] [ 5048] [depth= 8] . ( 26 sec) [ -22333.7500] [ 5042] [depth= 1] . ( 26 sec) [ -22310.8335] [ 5029] [depth= 5] . ( 26 sec) [ -22286.0960] [ 5023] [depth= 22] . ( 26 sec) [ -22210.6977] [ 5012] [depth= 4] . ( 26 sec) [ -22193.3834] [ 5013] [depth= 1] . ( 26 sec) [ -22155.9718] [ 5007] [depth= 22] . ( 27 sec) [ -22109.5208] [ 4997] [depth= 18] . ( 27 sec) [ -22046.4840] [ 4985] [depth= 10] . ( 27 sec) [ -21986.8989] [ 4984] [depth= 2] . ( 27 sec) [ -21903.6075] [ 4928] [depth= 22] . ( 27 sec) [ -21881.7025] [ 4920] [depth= 6] . ( 28 sec) [ -21770.0632] [ 4897] [depth= 17] . ( 28 sec) [ -21657.0413] [ 4867] [depth= 10] . ( 28 sec) [ -21629.9479] [ 4854] [depth= 1] . ( 28 sec) [ -21621.1843] [ 4854] [depth= 1] . ( 29 sec) [ -21403.2920] [ 4784] [depth= 8] . ( 29 sec) [ -21378.7646] [ 4779] [depth= 16] . ( 29 sec) [ -21361.8631] [ 4778] [depth= 1] . ( 29 sec) [ -21299.7561] [ 4768] [depth= 9] . ( 29 sec) [ -21288.5277] [ 4767] [depth= 1] . ( 30 sec) [ -21256.3454] [ 4763] [depth= 2] . ( 30 sec) [ -21214.2864] [ 4745] [depth= 1] . ( 30 sec) [ -21160.3146] [ 4732] [depth= 5] . ( 30 sec) [ -21117.5810] [ 4719] [depth= 5] . ( 30 sec) [ -21106.8293] [ 4720] [depth= 1] . ( 30 sec) [ -21096.3250] [ 4719] [depth= 2] . ( 31 sec) [ -21028.6127] [ 4702] [depth= 5] . ( 31 sec) [ -21005.7015] [ 4678] [depth= 6] . ( 31 sec) [ -20993.0217] [ 4678] [depth= 1] . ( 31 sec) [ -20919.2655] [ 4661] [depth= 8] . ( 31 sec) [ -20860.6001] [ 4656] [depth= 9] . ( 31 sec) [ -20816.3543] [ 4656] [depth= 2] . ( 32 sec) [ -20637.1903] [ 4525] [depth= 16] . ( 32 sec) [ -20634.0763] [ 4522] [depth= 9] . ( 32 sec) [ -20617.5285] [ 4520] [depth= 2] . ( 32 sec) [ -20609.9939] [ 4520] [depth= 1] . ( 32 sec) [ -20595.2589] [ 4520] [depth= 1] . ( 33 sec) [ -20585.5656] [ 4519] [depth= 7] . ( 33 sec) [ -20560.3185] [ 4513] [depth= 15] . ( 33 sec) [ -20549.0029] [ 4518] [depth= 1] . ( 33 sec) [ -20413.9033] [ 4476] [depth= 7] . ( 33 sec) [ -20399.1023] [ 4476] [depth= 1] . ( 33 sec) [ -20317.8732] [ 4463] [depth= 12] . ( 34 sec) [ -20195.1601] [ 4429] [depth= 2] . ( 34 sec) [ -20083.2805] [ 4414] [depth= 14] . ( 34 sec) [ -20036.1807] [ 4414] [depth= 1] . ( 34 sec) [ -19928.8357] [ 4384] [depth= 9] . ( 34 sec) [ -19433.2090] [ 4315] [depth= 5] . ( 34 sec) [ -19291.5222] [ 4219] [depth= 17] . ( 35 sec) [ -19280.7750] [ 4218] [depth= 1] . ( 35 sec) [ -19256.8943] [ 4217] [depth= 3] . ( 35 sec) [ -19231.9053] [ 4213] [depth= 3] . ( 35 sec) [ -19223.6137] [ 4208] [depth= 12] . ( 35 sec) [ -19221.2223] [ 4208] [depth= 1] . ( 36 sec) [ -19218.2316] [ 4203] [depth= 7] . ( 36 sec) [ -19212.3582] [ 4202] [depth= 1] . ( 36 sec) [ -19106.0123] [ 4200] [depth= 2] . ( 36 sec) [ -19095.4459] [ 4199] [depth= 2] . ( 36 sec) [ -19091.6109] [ 4195] [depth= 7] . ( 36 sec) [ -19072.8650] [ 4194] [depth= 1] . ( 37 sec) [ -19072.5209] [ 4193] [depth= 1] . ( 37 sec) [ -19071.2137] [ 4192] [depth= 1] . ( 37 sec) [ -19069.2384] [ 4190] [depth= 13] . ( 37 sec) [ -19003.9935] [ 4177] [depth= 8] . ( 38 sec) [ -18967.1331] [ 4169] [depth= 7] . ( 38 sec) [ -18962.2746] [ 4168] [depth= 1] . ( 38 sec) [ -18962.0703] [ 4168] [depth= 1] . ( 38 sec) [ -18892.8630] [ 4163] [depth= 4] . ( 38 sec) [ -18891.5358] [ 4164] [depth= 1] . ( 38 sec) [ -18828.1603] [ 4164] [depth= 2] . ( 39 sec) [ -18744.4202] [ 4148] [depth= 8] . ( 39 sec) [ -18740.4657] [ 4148] [depth= 1] . ( 39 sec) [ -18708.2577] [ 4141] [depth= 6] . ( 40 sec) [ -18677.5932] [ 4140] [depth= 9] . ( 40 sec) [ -18666.9189] [ 4145] [depth= 1] . ( 40 sec) [ -18661.9385] [ 4143] [depth= 1] . ( 40 sec) [ -18655.1391] [ 4143] [depth= 2] . ( 41 sec) [ -18534.4700] [ 4084] [depth= 8] . ( 42 sec) [ -18487.6566] [ 4080] [depth= 1] . ( 42 sec) [ -18473.6605] [ 4080] [depth= 2] . ( 42 sec) [ -18439.3968] [ 4076] [depth= 1] . ( 42 sec) [ -18103.4021] [ 4079] [depth= 18] . ( 43 sec) [ -18102.5545] [ 4081] [depth= 3] . ( 43 sec) [ -18087.8659] [ 4080] [depth= 4] . ( 43 sec) [ -18086.5074] [ 4090] [depth= 1] . ( 44 sec) [ -18082.6848] [ 4088] [depth= 3] . ( 44 sec) [ -18080.4418] [ 4087] [depth= 4] . ( 44 sec) [ -18078.8419] [ 4086] [depth= 1] . ( 44 sec) [ -18076.7815] [ 4083] [depth= 4] . ( 45 sec) [ -18072.6579] [ 4077] [depth= 5] . ( 45 sec) [ -18051.9270] [ 4078] [depth= 1] . ( 45 sec) [ -18036.4329] [ 4057] [depth= 5] . ( 46 sec) [ -17906.4454] [ 4026] [depth= 15] . ( 46 sec) [ -17906.4234] [ 4027] [depth= 1] . ( 46 sec) [ -17905.6414] [ 4027] [depth= 1] . ( 46 sec) [ -17851.6628] [ 4016] [depth= 4] . ( 47 sec) [ -17841.0861] [ 4016] [depth= 1] . ( 47 sec) [ -17839.6398] [ 4018] [depth= 1] . ( 47 sec) [ -17829.5350] [ 4016] [depth= 1] . ( 47 sec) [ -17678.6211] [ 3909] [depth= 12] . ( 47 sec) [ -17647.0223] [ 3896] [depth= 1] . ( 47 sec) [ -17512.3633] [ 3830] [depth= 1] . ( 48 sec) [ -17486.8276] [ 3790] [depth= 6] . ( 48 sec) [ -17477.6345] [ 3786] [depth= 3] . ( 48 sec) [ -17435.1172] [ 3775] [depth= 1] . ( 48 sec) [ -17413.1684] [ 3786] [depth= 1] . ( 48 sec) [ -17396.0694] [ 3781] [depth= 6] . ( 49 sec) [ -17384.6112] [ 3778] [depth= 3] . ( 49 sec) [ -17358.9890] [ 3766] [depth= 1] . ( 49 sec) [ -17307.4456] [ 3754] [depth= 2] . ( 49 sec) [ -17273.3147] [ 3718] [depth= 10] . ( 49 sec) [ -17270.1296] [ 3716] [depth= 2] . ( 50 sec) [ -17259.0821] [ 3713] [depth= 2] . ( 50 sec) [ -17109.1443] [ 3668] [depth= 4] . ( 50 sec) [ -17105.4103] [ 3668] [depth= 1] . ( 50 sec) [ -17105.2186] [ 3668] [depth= 1] . ( 51 sec) [ -17102.3347] [ 3667] [depth= 1] . ( 51 sec) [ -17097.0066] [ 3666] [depth= 1] . ( 51 sec) [ -17025.8983] [ 3650] [depth= 2] . ( 51 sec) [ -17022.7283] [ 3649] [depth= 2] . ( 51 sec) [ -16954.3459] [ 3614] [depth= 7] . ( 52 sec) [ -16872.9602] [ 3611] [depth= 2] . ( 52 sec) [ -16623.1321] [ 3498] [depth= 2] . ( 53 sec) [ -16622.6431] [ 3495] [depth= 4] . ( 53 sec) [ -16622.0763] [ 3495] [depth= 1] . ( 54 sec) [ -16603.9270] [ 3498] [depth= 6] . ( 54 sec) [ -16537.3939] [ 3436] [depth= 11] . ( 54 sec) [ -16535.1382] [ 3445] [depth= 1] . ( 55 sec) [ -16507.4998] [ 3451] [depth= 1] . ( 56 sec) [ -16075.7752] [Branch lengths ] . ( 64 sec) [ -16034.8226] [GTR parameters ] . ( 65 sec) [ -16034.8010] [Alpha ][ 0.505764] . ( 67 sec) [ -16028.5706] [ 3447] [depth= 5] . ( 68 sec) [ -16027.4452] [ 3446] [depth= 1] . ( 68 sec) [ -15967.8743] [ 3381] [depth= 8] . ( 68 sec) [ -15958.0290] [ 3376] [depth= 1] . ( 68 sec) [ -15944.0966] [ 3369] [depth= 1] . ( 68 sec) [ -15941.5747] [ 3366] [depth= 1] . ( 68 sec) [ -15941.1425] [ 3367] [depth= 2] . ( 69 sec) [ -15939.7206] [ 3367] [depth= 1] . ( 69 sec) [ -15937.7405] [ 3369] [depth= 1] . ( 69 sec) [ -15932.4195] [ 3368] [depth= 2] . ( 71 sec) [ -15929.4372] [ 3366] [depth= 2] . ( 71 sec) [ -15896.9991] [ 3358] [depth= 1] . ( 71 sec) [ -15896.5848] [ 3358] [depth= 1] . ( 72 sec) [ -15884.1888] [ 3346] [depth= 2] . ( 73 sec) [ -15857.8865] [ 3310] [depth= 9] . ( 73 sec) [ -15855.4625] [ 3308] [depth= 2] . ( 74 sec) [ -15850.9995] [ 3307] [depth= 1] . ( 74 sec) [ -15850.5355] [ 3301] [depth= 1] . ( 75 sec) [ -15847.5304] [ 3301] [depth= 3] . ( 77 sec) [ -15846.2038] [ 3292] [depth= 1] . ( 80 sec) [ -15811.1221] [ 3275] [depth= 2] . ( 81 sec) [ -15809.8811] [ 3276] [depth= 1] . ( 82 sec) [ -15809.6330] [ 3276] [depth= 1] . ( 83 sec) [ -15808.0569] [ 3276] [depth= 1] . ( 85 sec) [ -15804.2802] [ 3275] [depth= 3] . ( 85 sec) [ -15787.9033] [ 3242] [depth= 1] . ( 86 sec) [ -15787.6484] [ 3243] [depth= 1] . ( 87 sec) [ -15786.9806] [ 3241] [depth= 3] . ( 88 sec) [ -15786.6490] [ 3241] [depth= 1] . ( 89 sec) [ -15782.7280] [ 3240] [depth= 1] . ( 92 sec) [ -15761.2080] [ 3225] [depth= 8] . ( 92 sec) [ -15744.9342] [ 3203] [depth= 1] . ( 96 sec) [ -15740.5501] [ 3202] [depth= 1] . ( 105 sec) [ -15739.7116] [ 3207] [depth= 1] . ( 106 sec) [ -15738.9857] [ 3207] [depth= 1] . ( 106 sec) [ -15738.9615] [ 3206] [depth= 1] . ( 106 sec) [ -15738.8523] [ 3205] [depth= 1] . ( 108 sec) [ -15738.4298] [ 3208] [depth= 1] . ( 109 sec) [ -15736.4004] [ 3210] [depth= 1] . ( 112 sec) [ -15736.3762] [ 3210] [depth= 1] . ( 113 sec) [ -15736.3394] [ 3211] [depth= 1] . ( 117 sec) [ -15735.1306] [ 3213] [depth= 1] . ( 120 sec) [ -15729.9167] [ 3209] [depth= 1] . ( 121 sec) [ -15676.4145] [Branch lengths ] . ( 127 sec) [ -15675.9338] [GTR parameters ] . ( 127 sec) [ -15675.0548] [Alpha ][ 0.537901] . ( 128 sec) [ -15670.6133] [ 3206] [depth= 1] . ( 140 sec) [ -15669.9077] [ 3203] [depth= 1] . ( 141 sec) [ -15668.6053] [ 3201] [depth= 1] . ( 142 sec) [ -15668.2828] [ 3197] [depth= 1] . ( 172 sec) [ -15668.0343] [ 3201] [depth= 1] . ( 174 sec) [ -15667.8679] [ 3200] [depth= 1] . ( 190 sec) [ -15660.8806] [Branch lengths ] . ( 195 sec) [ -15660.8220] [GTR parameters ] . ( 195 sec) [ -15660.7895] [Alpha ][ 0.544527] . ( 253 sec) [ -15660.3509] [Branch lengths ] . ( 260 sec) [ -15660.2902] [ 3200] [depth= 2] . ( 296 sec) [ -15660.2600] [ 3200] [depth= 1] . ( 300 sec) [ -15660.1641] [ 3200] [depth= 1] . ( 365 sec) [ -15660.0412] [ 3197] [depth= 1] . ( 406 sec) [ -15659.5032] [Branch lengths ] . ( 410 sec) [ -15659.4962] [GTR parameters ] . ( 411 sec) [ -15659.4956] [Alpha ][ 0.545367] . ( 411 sec) [ -15659.4956] [Topology ] . ( 414 sec) [ -15659.4222] [Topology ] . ( 418 sec) [ -15659.3948] [Topology ] . ( 421 sec) [ -15659.3776] [Topology ] . ( 425 sec) [ -15659.3652] [Topology ] . ( 429 sec) [ -15659.3557] [Topology ] . ( 432 sec) [ -15659.3482] [Topology ] . ( 435 sec) [ -15659.3466] [GTR parameters ] . ( 436 sec) [ -15659.3465] [Alpha ][ 0.545912] . ( 436 sec) [ -15659.3465] [Topology ] . ( 439 sec) [ -15659.3397] [Topology ] . ( 443 sec) [ -15659.3342] [Topology ] . ( 446 sec) [ -15659.3296] [Topology ] . ( 450 sec) [ -15659.3258] [Topology ] . ( 454 sec) [ -15659.3224] [Topology ] . ( 457 sec) [ -15659.3194] [Topology ] . ( 459 sec) [ -15659.3191] [GTR parameters ] . ( 459 sec) [ -15659.3191] [Alpha ][ 0.545912] . ( 459 sec) [ -15659.3191] [Topology ] . ( 463 sec) [ -15659.3164] [Topology ] . ( 466 sec) [ -15659.3139] [Topology ] . ( 470 sec) [ -15659.3115] [Topology ] . ( 473 sec) [ -15659.3094] [Topology ] . ( 477 sec) [ -15659.3073] [Topology ] . ( 481 sec) [ -15659.3058] [Topology ] . ( 481 sec) [ -15659.3058] [GTR parameters ] . ( 482 sec) [ -15659.3058] [Alpha ][ 0.545912] . ( 482 sec) [ -15659.3058] [Topology ] . ( 485 sec) [ -15659.3050] [Topology ] . ( 487 sec) [ -15659.3048] [GTR parameters ] . ( 488 sec) [ -15659.3048] [Alpha ][ 0.545912] . Checking for NNIs, optimizing five branches... . ( 514 sec) [ -15659.3042] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15659.304165. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -37225.6455] [GTR parameters ] . ( 7 sec) [ -36416.3751] [Alpha ][ 0.500960] . ( 7 sec) [ -36031.3227] [ 7047] [depth= 11] . ( 7 sec) [ -35501.3808] [ 6991] [depth= 10] . ( 8 sec) [ -35498.7435] [ 6988] [depth= 6] . ( 8 sec) [ -35477.6812] [ 6983] [depth= 1] . ( 8 sec) [ -35458.3770] [ 6970] [depth= 9] . ( 8 sec) [ -35116.0798] [ 6959] [depth= 2] . ( 8 sec) [ -35021.8620] [ 6940] [depth= 7] . ( 8 sec) [ -34989.2816] [ 6830] [depth= 3] . ( 9 sec) [ -34925.2588] [ 6822] [depth= 12] . ( 9 sec) [ -34903.0510] [ 6820] [depth= 2] . ( 9 sec) [ -34881.2009] [ 6818] [depth= 2] . ( 9 sec) [ -34866.7810] [ 6804] [depth= 8] . ( 9 sec) [ -34819.6781] [ 6799] [depth= 13] . ( 9 sec) [ -34659.6380] [ 6772] [depth= 13] . ( 10 sec) [ -34614.2764] [ 6770] [depth= 7] . ( 10 sec) [ -34606.5896] [ 6766] [depth= 22] . ( 10 sec) [ -34565.1008] [ 6748] [depth= 8] . ( 10 sec) [ -34530.0370] [ 6747] [depth= 1] . ( 10 sec) [ -34458.8607] [ 6733] [depth= 17] . ( 11 sec) [ -34380.0183] [ 6718] [depth= 4] . ( 11 sec) [ -34297.0071] [ 6708] [depth= 5] . ( 11 sec) [ -34005.4481] [ 6663] [depth= 21] . ( 11 sec) [ -33970.9254] [ 6665] [depth= 19] . ( 11 sec) [ -33899.3102] [ 6646] [depth= 17] . ( 11 sec) [ -33876.1537] [ 6648] [depth= 5] . ( 12 sec) [ -33866.9331] [ 6647] [depth= 3] . ( 12 sec) [ -33848.1726] [ 6635] [depth= 5] . ( 12 sec) [ -33847.6849] [ 6633] [depth= 1] . ( 12 sec) [ -33828.7301] [ 6631] [depth= 1] . ( 12 sec) [ -33785.4074] [ 6621] [depth= 6] . ( 12 sec) [ -33156.3183] [ 6572] [depth= 2] . ( 13 sec) [ -32939.8211] [ 6561] [depth= 3] . ( 13 sec) [ -32896.9460] [ 6559] [depth= 2] . ( 13 sec) [ -32828.4713] [ 6550] [depth= 18] . ( 13 sec) [ -32823.7203] [ 6554] [depth= 1] . ( 13 sec) [ -32728.2789] [ 6554] [depth= 1] . ( 13 sec) [ -32563.6277] [ 6536] [depth= 12] . ( 14 sec) [ -32420.1353] [ 6517] [depth= 4] . ( 14 sec) [ -32366.9242] [ 6506] [depth= 25] . ( 14 sec) [ -32282.5662] [ 6444] [depth= 6] . ( 14 sec) [ -32199.8955] [ 6436] [depth= 2] . ( 14 sec) [ -32146.7942] [ 6434] [depth= 1] . ( 15 sec) [ -31804.7802] [ 6395] [depth= 7] . ( 15 sec) [ -31671.2127] [ 6371] [depth= 6] . ( 15 sec) [ -31525.3494] [ 6316] [depth= 1] . ( 15 sec) [ -31305.6143] [ 6243] [depth= 25] . ( 15 sec) [ -31137.2586] [ 6322] [depth= 27] . ( 15 sec) [ -31073.1771] [ 6312] [depth= 10] . ( 16 sec) [ -31051.2927] [ 6317] [depth= 1] . ( 16 sec) [ -30934.6743] [ 6285] [depth= 2] . ( 16 sec) [ -30668.6924] [ 6241] [depth= 11] . ( 16 sec) [ -30520.0987] [ 6170] [depth= 14] . ( 16 sec) [ -30333.0354] [ 6167] [depth= 11] . ( 17 sec) [ -30280.6030] [ 6160] [depth= 17] . ( 17 sec) [ -30172.4761] [ 6126] [depth= 31] . ( 17 sec) [ -30086.3474] [ 6112] [depth= 20] . ( 17 sec) [ -30012.1494] [ 6105] [depth= 12] . ( 17 sec) [ -29975.0189] [ 6095] [depth= 16] . ( 18 sec) [ -29469.0902] [ 6086] [depth= 12] . ( 18 sec) [ -29442.9851] [ 6079] [depth= 2] . ( 18 sec) [ -29413.0163] [ 6080] [depth= 1] . ( 18 sec) [ -29353.3728] [ 6076] [depth= 3] . ( 18 sec) [ -29298.6071] [ 6065] [depth= 3] . ( 18 sec) [ -29115.0629] [ 6079] [depth= 2] . ( 18 sec) [ -29076.1247] [ 6073] [depth= 19] . ( 19 sec) [ -28828.0804] [ 5944] [depth= 2] . ( 19 sec) [ -28411.8669] [ 5910] [depth= 12] . ( 19 sec) [ -28324.0065] [ 5886] [depth= 3] . ( 19 sec) [ -28035.7252] [ 5825] [depth= 16] . ( 19 sec) [ -28030.2046] [ 5818] [depth= 8] . ( 19 sec) [ -28014.4489] [ 5818] [depth= 1] . ( 20 sec) [ -27998.4698] [ 5816] [depth= 8] . ( 20 sec) [ -27946.1774] [ 5793] [depth= 9] . ( 20 sec) [ -27836.4503] [ 5775] [depth= 10] . ( 20 sec) [ -27818.7129] [ 5777] [depth= 5] . ( 21 sec) [ -27801.9044] [ 5772] [depth= 11] . ( 21 sec) [ -27788.9019] [ 5767] [depth= 1] . ( 21 sec) [ -27781.6526] [ 5759] [depth= 13] . ( 21 sec) [ -27747.4604] [ 5759] [depth= 2] . ( 21 sec) [ -27713.6525] [ 5759] [depth= 17] . ( 22 sec) [ -27435.8695] [ 5748] [depth= 10] . ( 22 sec) [ -27425.2792] [ 5743] [depth= 1] . ( 22 sec) [ -27390.3726] [ 5740] [depth= 2] . ( 22 sec) [ -27377.7997] [ 5744] [depth= 2] . ( 22 sec) [ -27280.4117] [ 5721] [depth= 5] . ( 22 sec) [ -27148.3651] [ 5687] [depth= 14] . ( 23 sec) [ -27051.1551] [ 5666] [depth= 5] . ( 23 sec) [ -27025.9447] [ 5666] [depth= 3] . ( 23 sec) [ -26918.4760] [ 5651] [depth= 13] . ( 23 sec) [ -26883.4024] [ 5645] [depth= 1] . ( 23 sec) [ -26828.5114] [ 5628] [depth= 6] . ( 24 sec) [ -26762.2870] [ 5619] [depth= 7] . ( 24 sec) [ -26731.0332] [ 5613] [depth= 2] . ( 24 sec) [ -26605.8355] [ 5477] [depth= 13] . ( 24 sec) [ -26201.5799] [ 5475] [depth= 1] . ( 25 sec) [ -25756.0780] [ 5318] [depth= 17] . ( 25 sec) [ -25753.1642] [ 5323] [depth= 1] . ( 25 sec) [ -25740.8438] [ 5326] [depth= 1] . ( 25 sec) [ -25677.7284] [ 5322] [depth= 4] . ( 25 sec) [ -25563.2466] [ 5296] [depth= 1] . ( 26 sec) [ -25466.2147] [ 5280] [depth= 5] . ( 26 sec) [ -25447.1962] [ 5276] [depth= 4] . ( 26 sec) [ -25429.0648] [ 5269] [depth= 12] . ( 26 sec) [ -25419.3213] [ 5270] [depth= 1] . ( 26 sec) [ -25332.1591] [ 5268] [depth= 18] . ( 26 sec) [ -25328.5814] [ 5265] [depth= 17] . ( 27 sec) [ -25272.6671] [ 5263] [depth= 1] . ( 27 sec) [ -25122.4975] [ 5178] [depth= 15] . ( 27 sec) [ -25053.6482] [ 5154] [depth= 2] . ( 27 sec) [ -25050.9866] [ 5154] [depth= 1] . ( 27 sec) [ -24598.0052] [ 5097] [depth= 15] . ( 28 sec) [ -24595.7401] [ 5104] [depth= 1] . ( 28 sec) [ -24516.6303] [ 5080] [depth= 14] . ( 28 sec) [ -24457.8335] [ 5077] [depth= 20] . ( 28 sec) [ -24164.9031] [ 4964] [depth= 23] . ( 28 sec) [ -24134.3673] [ 4945] [depth= 13] . ( 29 sec) [ -23902.6378] [ 4912] [depth= 7] . ( 29 sec) [ -23877.8866] [ 4894] [depth= 10] . ( 29 sec) [ -23827.6796] [ 4873] [depth= 12] . ( 29 sec) [ -23190.1312] [ 4749] [depth= 11] . ( 29 sec) [ -23129.6721] [ 4685] [depth= 5] . ( 30 sec) [ -23113.7964] [ 4682] [depth= 2] . ( 30 sec) [ -23085.4358] [ 4680] [depth= 5] . ( 30 sec) [ -23084.0643] [ 4680] [depth= 1] . ( 30 sec) [ -22993.7513] [ 4657] [depth= 4] . ( 30 sec) [ -22635.8027] [ 4535] [depth= 10] . ( 31 sec) [ -22565.6981] [ 4493] [depth= 12] . ( 31 sec) [ -22562.4943] [ 4488] [depth= 4] . ( 31 sec) [ -22554.1342] [ 4492] [depth= 1] . ( 31 sec) [ -22550.1071] [ 4488] [depth= 3] . ( 32 sec) [ -22537.9450] [ 4485] [depth= 4] . ( 32 sec) [ -22537.2649] [ 4483] [depth= 2] . ( 32 sec) [ -22525.7058] [ 4479] [depth= 5] . ( 32 sec) [ -22513.7571] [ 4477] [depth= 10] . ( 32 sec) [ -22457.2383] [ 4457] [depth= 9] . ( 33 sec) [ -22350.0509] [ 4406] [depth= 23] . ( 33 sec) [ -22246.8571] [ 4385] [depth= 23] . ( 33 sec) [ -22205.1256] [ 4373] [depth= 16] . ( 33 sec) [ -22090.6505] [ 4366] [depth= 1] . ( 34 sec) [ -21407.8065] [ 4304] [depth= 20] . ( 34 sec) [ -21406.0489] [ 4305] [depth= 1] . ( 34 sec) [ -21347.3742] [ 4292] [depth= 14] . ( 34 sec) [ -21340.8164] [ 4295] [depth= 18] . ( 35 sec) [ -21267.4043] [ 4282] [depth= 8] . ( 35 sec) [ -21262.7189] [ 4281] [depth= 2] . ( 35 sec) [ -21254.9775] [ 4276] [depth= 6] . ( 35 sec) [ -21149.6509] [ 4277] [depth= 9] . ( 36 sec) [ -21147.6794] [ 4277] [depth= 1] . ( 36 sec) [ -21054.7386] [ 4245] [depth= 5] . ( 36 sec) [ -21044.9075] [ 4247] [depth= 1] . ( 36 sec) [ -20948.7954] [ 4217] [depth= 3] . ( 36 sec) [ -20875.4190] [ 4208] [depth= 18] . ( 36 sec) [ -20767.2509] [ 4207] [depth= 2] . ( 37 sec) [ -20665.9062] [ 4224] [depth= 1] . ( 37 sec) [ -20552.6340] [ 4185] [depth= 27] . ( 37 sec) [ -20545.9566] [ 4178] [depth= 1] . ( 37 sec) [ -20046.6346] [ 4067] [depth= 23] . ( 38 sec) [ -19615.9545] [ 3991] [depth= 1] . ( 38 sec) [ -19566.2424] [ 3986] [depth= 2] . ( 38 sec) [ -19533.8175] [ 3984] [depth= 1] . ( 38 sec) [ -19514.0894] [ 3983] [depth= 1] . ( 38 sec) [ -19463.0247] [ 3966] [depth= 1] . ( 38 sec) [ -19444.8835] [ 3968] [depth= 1] . ( 39 sec) [ -19311.1011] [ 3933] [depth= 17] . ( 39 sec) [ -19305.3951] [ 3936] [depth= 1] . ( 39 sec) [ -19283.9276] [ 3931] [depth= 1] . ( 39 sec) [ -19270.9674] [ 3933] [depth= 1] . ( 40 sec) [ -19241.9933] [ 3929] [depth= 2] . ( 40 sec) [ -19235.8790] [ 3929] [depth= 1] . ( 40 sec) [ -19226.1332] [ 3928] [depth= 3] . ( 40 sec) [ -19223.5062] [ 3924] [depth= 4] . ( 40 sec) [ -19220.9114] [ 3923] [depth= 4] . ( 41 sec) [ -19162.1431] [ 3938] [depth= 1] . ( 41 sec) [ -18668.2414] [ 3927] [depth= 3] . ( 41 sec) [ -18448.8848] [ 3894] [depth= 2] . ( 41 sec) [ -18393.1539] [ 3892] [depth= 3] . ( 41 sec) [ -18374.6598] [ 3887] [depth= 11] . ( 41 sec) [ -18360.4069] [ 3885] [depth= 1] . ( 42 sec) [ -18359.7689] [ 3886] [depth= 1] . ( 42 sec) [ -18351.0220] [ 3887] [depth= 2] . ( 42 sec) [ -18349.9077] [ 3878] [depth= 2] . ( 42 sec) [ -18341.0126] [ 3872] [depth= 1] . ( 42 sec) [ -18272.3486] [ 3867] [depth= 7] . ( 42 sec) [ -18271.9657] [ 3869] [depth= 1] . ( 43 sec) [ -18259.4277] [ 3863] [depth= 2] . ( 43 sec) [ -18251.5323] [ 3862] [depth= 5] . ( 43 sec) [ -18039.3214] [ 3819] [depth= 15] . ( 43 sec) [ -18027.4067] [ 3826] [depth= 1] . ( 44 sec) [ -18019.5964] [ 3830] [depth= 1] . ( 44 sec) [ -18016.5900] [ 3823] [depth= 1] . ( 44 sec) [ -18014.0463] [ 3820] [depth= 3] . ( 44 sec) [ -17848.6658] [ 3728] [depth= 2] . ( 44 sec) [ -17848.6536] [ 3728] [depth= 4] . ( 44 sec) [ -17847.6465] [ 3728] [depth= 3] . ( 45 sec) [ -17843.6957] [ 3728] [depth= 1] . ( 45 sec) [ -17801.9470] [ 3707] [depth= 3] . ( 45 sec) [ -17789.9982] [ 3706] [depth= 11] . ( 45 sec) [ -17778.1676] [ 3702] [depth= 1] . ( 45 sec) [ -17776.9874] [ 3702] [depth= 4] . ( 46 sec) [ -17759.6302] [ 3700] [depth= 1] . ( 46 sec) [ -17755.3235] [ 3701] [depth= 2] . ( 46 sec) [ -17750.0739] [ 3688] [depth= 1] . ( 46 sec) [ -17719.3502] [ 3682] [depth= 2] . ( 46 sec) [ -17717.3374] [ 3682] [depth= 2] . ( 47 sec) [ -17712.4851] [ 3679] [depth= 1] . ( 47 sec) [ -17704.2680] [ 3672] [depth= 5] . ( 47 sec) [ -17703.7271] [ 3674] [depth= 1] . ( 47 sec) [ -17682.1870] [ 3669] [depth= 8] . ( 48 sec) [ -17673.5996] [ 3665] [depth= 12] . ( 48 sec) [ -17670.6841] [ 3666] [depth= 2] . ( 48 sec) [ -17639.9072] [ 3676] [depth= 1] . ( 48 sec) [ -17589.2253] [ 3676] [depth= 1] . ( 49 sec) [ -17585.0904] [ 3679] [depth= 1] . ( 49 sec) [ -17546.8886] [ 3679] [depth= 3] . ( 49 sec) [ -17542.6505] [ 3672] [depth= 4] . ( 49 sec) [ -17541.5331] [ 3669] [depth= 1] . ( 49 sec) [ -17536.8271] [ 3669] [depth= 1] . ( 50 sec) [ -17524.7602] [ 3666] [depth= 3] . ( 50 sec) [ -17514.7183] [ 3668] [depth= 1] . ( 50 sec) [ -17442.0874] [ 3652] [depth= 1] . ( 50 sec) [ -17187.9300] [ 3656] [depth= 1] . ( 51 sec) [ -17028.2226] [ 3541] [depth= 10] . ( 51 sec) [ -17018.2531] [ 3541] [depth= 1] . ( 51 sec) [ -17007.3944] [ 3539] [depth= 8] . ( 51 sec) [ -16972.4648] [ 3540] [depth= 1] . ( 52 sec) [ -16963.5224] [ 3539] [depth= 3] . ( 52 sec) [ -16962.1558] [ 3542] [depth= 1] . ( 52 sec) [ -16946.2618] [ 3539] [depth= 2] . ( 52 sec) [ -16920.9318] [ 3536] [depth= 2] . ( 53 sec) [ -16910.4362] [ 3539] [depth= 2] . ( 53 sec) [ -16895.6894] [ 3530] [depth= 2] . ( 53 sec) [ -16871.5754] [ 3532] [depth= 1] . ( 53 sec) [ -16856.9014] [ 3530] [depth= 1] . ( 54 sec) [ -16855.6908] [ 3530] [depth= 1] . ( 55 sec) [ -16518.7274] [Branch lengths ] . ( 62 sec) [ -16484.0405] [GTR parameters ] . ( 63 sec) [ -16484.0325] [Alpha ][ 0.497942] . ( 63 sec) [ -16427.2669] [ 3502] [depth= 1] . ( 63 sec) [ -16392.6010] [ 3495] [depth= 13] . ( 64 sec) [ -16391.7707] [ 3494] [depth= 2] . ( 64 sec) [ -16391.4642] [ 3495] [depth= 3] . ( 65 sec) [ -16378.1916] [ 3493] [depth= 6] . ( 65 sec) [ -16375.5839] [ 3492] [depth= 2] . ( 65 sec) [ -16284.9765] [ 3457] [depth= 13] . ( 66 sec) [ -16283.5847] [ 3456] [depth= 2] . ( 66 sec) [ -16283.2215] [ 3452] [depth= 1] . ( 66 sec) [ -16275.7492] [ 3453] [depth= 1] . ( 67 sec) [ -16258.3030] [ 3452] [depth= 1] . ( 67 sec) [ -16253.5679] [ 3452] [depth= 1] . ( 67 sec) [ -16246.3900] [ 3449] [depth= 3] . ( 67 sec) [ -16246.1010] [ 3451] [depth= 1] . ( 68 sec) [ -16246.0489] [ 3451] [depth= 1] . ( 68 sec) [ -16244.8705] [ 3450] [depth= 1] . ( 68 sec) [ -16195.7703] [ 3392] [depth= 8] . ( 68 sec) [ -16169.8851] [ 3382] [depth= 1] . ( 70 sec) [ -16168.6510] [ 3380] [depth= 5] . ( 70 sec) [ -16168.5543] [ 3381] [depth= 1] . ( 71 sec) [ -16164.6139] [ 3382] [depth= 2] . ( 71 sec) [ -16107.4695] [ 3353] [depth= 14] . ( 72 sec) [ -16107.1706] [ 3353] [depth= 1] . ( 72 sec) [ -16075.4177] [ 3339] [depth= 4] . ( 73 sec) [ -16058.6517] [ 3333] [depth= 4] . ( 73 sec) [ -16047.8024] [ 3330] [depth= 3] . ( 73 sec) [ -16047.3495] [ 3328] [depth= 1] . ( 73 sec) [ -16043.3620] [ 3325] [depth= 1] . ( 73 sec) [ -16034.0520] [ 3316] [depth= 1] . ( 74 sec) [ -16027.7293] [ 3315] [depth= 2] . ( 74 sec) [ -16026.3231] [ 3316] [depth= 1] . ( 74 sec) [ -15997.7870] [ 3310] [depth= 3] . ( 74 sec) [ -15980.0531] [ 3312] [depth= 1] . ( 75 sec) [ -15979.9368] [ 3311] [depth= 1] . ( 75 sec) [ -15975.4670] [ 3311] [depth= 2] . ( 75 sec) [ -15971.0895] [ 3310] [depth= 1] . ( 76 sec) [ -15970.4587] [ 3311] [depth= 2] . ( 76 sec) [ -15936.5983] [ 3303] [depth= 3] . ( 76 sec) [ -15936.1565] [ 3302] [depth= 1] . ( 77 sec) [ -15935.5411] [ 3303] [depth= 1] . ( 77 sec) [ -15934.2770] [ 3303] [depth= 2] . ( 77 sec) [ -15906.9392] [ 3299] [depth= 3] . ( 78 sec) [ -15906.7346] [ 3301] [depth= 1] . ( 78 sec) [ -15903.3342] [ 3300] [depth= 5] . ( 80 sec) [ -15902.9219] [ 3297] [depth= 3] . ( 80 sec) [ -15899.6321] [ 3295] [depth= 1] . ( 81 sec) [ -15899.4661] [ 3295] [depth= 1] . ( 82 sec) [ -15894.3388] [ 3294] [depth= 1] . ( 82 sec) [ -15885.8861] [ 3290] [depth= 3] . ( 82 sec) [ -15885.6995] [ 3290] [depth= 1] . ( 82 sec) [ -15884.9027] [ 3290] [depth= 1] . ( 83 sec) [ -15879.5172] [ 3289] [depth= 1] . ( 83 sec) [ -15878.1565] [ 3288] [depth= 1] . ( 84 sec) [ -15870.3047] [ 3287] [depth= 2] . ( 85 sec) [ -15868.6597] [ 3288] [depth= 1] . ( 86 sec) [ -15866.8348] [ 3275] [depth= 6] . ( 86 sec) [ -15864.8486] [ 3275] [depth= 1] . ( 87 sec) [ -15862.0660] [ 3274] [depth= 1] . ( 87 sec) [ -15861.1013] [ 3273] [depth= 1] . ( 88 sec) [ -15854.1580] [ 3266] [depth= 1] . ( 88 sec) [ -15853.4346] [ 3266] [depth= 1] . ( 88 sec) [ -15852.6631] [ 3267] [depth= 1] . ( 88 sec) [ -15849.4777] [ 3266] [depth= 2] . ( 89 sec) [ -15849.0562] [ 3266] [depth= 1] . ( 89 sec) [ -15842.2414] [ 3260] [depth= 2] . ( 89 sec) [ -15842.1211] [ 3260] [depth= 1] . ( 90 sec) [ -15841.8194] [ 3261] [depth= 2] . ( 90 sec) [ -15804.1047] [ 3222] [depth= 9] . ( 90 sec) [ -15801.8009] [ 3217] [depth= 1] . ( 91 sec) [ -15797.3671] [ 3219] [depth= 1] . ( 91 sec) [ -15795.6136] [ 3217] [depth= 1] . ( 92 sec) [ -15794.3584] [ 3215] [depth= 1] . ( 93 sec) [ -15792.8961] [ 3215] [depth= 1] . ( 93 sec) [ -15791.6957] [ 3215] [depth= 1] . ( 93 sec) [ -15788.9498] [ 3216] [depth= 1] . ( 94 sec) [ -15788.2037] [ 3215] [depth= 1] . ( 94 sec) [ -15759.5946] [ 3202] [depth= 2] . ( 94 sec) [ -15756.7506] [ 3204] [depth= 1] . ( 94 sec) [ -15755.1112] [ 3207] [depth= 1] . ( 95 sec) [ -15754.6305] [ 3208] [depth= 1] . ( 95 sec) [ -15753.7866] [ 3206] [depth= 1] . ( 95 sec) [ -15751.7507] [ 3203] [depth= 1] . ( 96 sec) [ -15749.3331] [ 3200] [depth= 1] . ( 97 sec) [ -15747.0922] [ 3199] [depth= 1] . ( 98 sec) [ -15746.8827] [ 3199] [depth= 1] . ( 98 sec) [ -15742.2532] [ 3201] [depth= 1] . ( 98 sec) [ -15740.1788] [ 3201] [depth= 1] . ( 101 sec) [ -15739.0451] [ 3202] [depth= 1] . ( 102 sec) [ -15738.1885] [ 3202] [depth= 1] . ( 102 sec) [ -15738.0913] [ 3202] [depth= 1] . ( 102 sec) [ -15735.4216] [ 3204] [depth= 1] . ( 103 sec) [ -15735.2482] [ 3204] [depth= 1] . ( 103 sec) [ -15734.6843] [ 3207] [depth= 1] . ( 103 sec) [ -15733.5459] [ 3206] [depth= 1] . ( 104 sec) [ -15732.8810] [ 3206] [depth= 1] . ( 104 sec) [ -15731.7125] [ 3206] [depth= 1] . ( 106 sec) [ -15731.4324] [ 3205] [depth= 1] . ( 107 sec) [ -15731.2114] [ 3203] [depth= 2] . ( 107 sec) [ -15730.3965] [ 3201] [depth= 1] . ( 109 sec) [ -15680.8776] [Branch lengths ] . ( 115 sec) [ -15679.6722] [GTR parameters ] . ( 115 sec) [ -15678.3505] [Alpha ][ 0.537453] . ( 116 sec) [ -15677.2036] [ 3200] [depth= 4] . ( 116 sec) [ -15675.2702] [ 3199] [depth= 1] . ( 120 sec) [ -15675.0747] [ 3202] [depth= 1] . ( 128 sec) [ -15674.6105] [ 3199] [depth= 1] . ( 145 sec) [ -15673.7780] [ 3200] [depth= 1] . ( 151 sec) [ -15673.7326] [ 3200] [depth= 1] . ( 157 sec) [ -15673.7222] [ 3200] [depth= 1] . ( 171 sec) [ -15666.3305] [Branch lengths ] . ( 175 sec) [ -15666.3037] [GTR parameters ] . ( 175 sec) [ -15666.2824] [Alpha ][ 0.542779] . ( 231 sec) [ -15663.8645] [Branch lengths ] . ( 349 sec) [ -15663.6630] [ 3196] [depth= 1] . ( 393 sec) [ -15663.1278] [Branch lengths ] . ( 394 sec) [ -15663.1274] [GTR parameters ] . ( 395 sec) [ -15663.1239] [Alpha ][ 0.544926] . ( 395 sec) [ -15663.1239] [Topology ] . ( 398 sec) [ -15663.0939] [Topology ] . ( 402 sec) [ -15663.0799] [Topology ] . ( 405 sec) [ -15663.0700] [Topology ] . ( 409 sec) [ -15663.0625] [Topology ] . ( 413 sec) [ -15663.0564] [Topology ] . ( 416 sec) [ -15663.0515] [Topology ] . ( 418 sec) [ -15663.0507] [GTR parameters ] . ( 418 sec) [ -15663.0503] [Alpha ][ 0.545665] . ( 418 sec) [ -15663.0503] [Topology ] . ( 422 sec) [ -15663.0458] [Topology ] . ( 425 sec) [ -15663.0420] [Topology ] . ( 429 sec) [ -15663.0388] [Topology ] . ( 432 sec) [ -15663.0359] [Topology ] . ( 436 sec) [ -15663.0333] [Topology ] . ( 439 sec) [ -15663.0310] [Topology ] . ( 441 sec) [ -15663.0309] [GTR parameters ] . ( 441 sec) [ -15663.0309] [Alpha ][ 0.545665] . ( 441 sec) [ -15663.0309] [Topology ] . ( 445 sec) [ -15663.0287] [Topology ] . ( 448 sec) [ -15663.0267] [Topology ] . ( 452 sec) [ -15663.0247] [Topology ] . ( 455 sec) [ -15663.0228] [Topology ] . ( 459 sec) [ -15663.0209] [Topology ] . ( 462 sec) [ -15663.0191] [Topology ] . ( 463 sec) [ -15663.0191] [GTR parameters ] . ( 464 sec) [ -15663.0191] [Alpha ][ 0.546211] . ( 464 sec) [ -15663.0191] [Topology ] . ( 468 sec) [ -15663.0172] [Topology ] . ( 472 sec) [ -15663.0156] [Topology ] . ( 475 sec) [ -15663.0147] [Topology ] . ( 477 sec) [ -15663.0147] [GTR parameters ] . ( 477 sec) [ -15663.0147] [Alpha ][ 0.546211] . ( 477 sec) [ -15663.0147] [Topology ] . ( 481 sec) [ -15663.0143] [Topology ] . ( 482 sec) [ -15663.0143] [GTR parameters ] . ( 482 sec) [ -15663.0143] [Alpha ][ 0.546211] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15663.014278. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -37414.1259] [GTR parameters ] . ( 3 sec) [ -36565.3540] [Alpha ][ 0.500960] . ( 4 sec) [ -36295.8992] [ 7081] [depth= 1] . ( 4 sec) [ -35714.6867] [ 7032] [depth= 8] . ( 4 sec) [ -35610.5549] [ 7030] [depth= 1] . ( 4 sec) [ -35123.4693] [ 6965] [depth= 6] . ( 5 sec) [ -35087.0062] [ 6950] [depth= 10] . ( 5 sec) [ -35059.8563] [ 6938] [depth= 1] . ( 5 sec) [ -34859.9579] [ 6934] [depth= 13] . ( 5 sec) [ -34817.5866] [ 6929] [depth= 5] . ( 5 sec) [ -34780.4412] [ 6922] [depth= 5] . ( 5 sec) [ -34686.6817] [ 6903] [depth= 3] . ( 6 sec) [ -34685.8794] [ 6900] [depth= 6] . ( 6 sec) [ -34600.3807] [ 6890] [depth= 6] . ( 6 sec) [ -34596.7997] [ 6889] [depth= 1] . ( 6 sec) [ -34233.5410] [ 6877] [depth= 5] . ( 6 sec) [ -33925.9582] [ 6871] [depth= 2] . ( 7 sec) [ -33916.5707] [ 6868] [depth= 5] . ( 7 sec) [ -33816.5646] [ 6864] [depth= 2] . ( 7 sec) [ -33540.5011] [ 6836] [depth= 11] . ( 7 sec) [ -33449.6293] [ 6828] [depth= 17] . ( 7 sec) [ -33383.6734] [ 6816] [depth= 5] . ( 8 sec) [ -33283.6271] [ 6813] [depth= 7] . ( 8 sec) [ -33219.7294] [ 6811] [depth= 3] . ( 8 sec) [ -33119.5851] [ 6784] [depth= 13] . ( 8 sec) [ -32950.3021] [ 6776] [depth= 10] . ( 8 sec) [ -32806.6736] [ 6763] [depth= 2] . ( 9 sec) [ -32598.8734] [ 6754] [depth= 13] . ( 9 sec) [ -32467.8383] [ 6735] [depth= 18] . ( 9 sec) [ -32049.3592] [ 6717] [depth= 13] . ( 9 sec) [ -31914.3063] [ 6714] [depth= 1] . ( 9 sec) [ -31469.7688] [ 6624] [depth= 17] . ( 10 sec) [ -31221.0059] [ 6580] [depth= 20] . ( 10 sec) [ -31109.6458] [ 6619] [depth= 16] . ( 10 sec) [ -30931.5104] [ 6506] [depth= 15] . ( 10 sec) [ -30797.2330] [ 6470] [depth= 15] . ( 10 sec) [ -30735.0543] [ 6452] [depth= 12] . ( 11 sec) [ -30590.4885] [ 6444] [depth= 1] . ( 11 sec) [ -30556.0898] [ 6440] [depth= 7] . ( 11 sec) [ -29859.3134] [ 6399] [depth= 12] . ( 11 sec) [ -29748.9090] [ 6370] [depth= 4] . ( 11 sec) [ -29680.9852] [ 6311] [depth= 2] . ( 12 sec) [ -29491.6700] [ 6267] [depth= 13] . ( 12 sec) [ -29490.5047] [ 6270] [depth= 12] . ( 12 sec) [ -29368.7555] [ 6251] [depth= 11] . ( 12 sec) [ -29261.1569] [ 6221] [depth= 18] . ( 12 sec) [ -29169.7990] [ 6202] [depth= 11] . ( 13 sec) [ -29092.5827] [ 6186] [depth= 3] . ( 13 sec) [ -29024.4563] [ 6182] [depth= 2] . ( 13 sec) [ -28798.4943] [ 6116] [depth= 17] . ( 13 sec) [ -28571.2924] [ 6069] [depth= 8] . ( 13 sec) [ -28507.9603] [ 6073] [depth= 1] . ( 14 sec) [ -28279.5822] [ 5997] [depth= 1] . ( 14 sec) [ -28037.3207] [ 5952] [depth= 1] . ( 14 sec) [ -27954.9481] [ 5941] [depth= 10] . ( 14 sec) [ -27809.2905] [ 5921] [depth= 17] . ( 14 sec) [ -27662.0975] [ 5892] [depth= 4] . ( 15 sec) [ -27524.3178] [ 5804] [depth= 7] . ( 15 sec) [ -27511.5025] [ 5791] [depth= 6] . ( 15 sec) [ -27467.5973] [ 5785] [depth= 3] . ( 15 sec) [ -27456.8786] [ 5783] [depth= 5] . ( 15 sec) [ -27442.8172] [ 5778] [depth= 1] . ( 16 sec) [ -27422.8758] [ 5771] [depth= 8] . ( 16 sec) [ -27416.1993] [ 5765] [depth= 1] . ( 16 sec) [ -27393.7596] [ 5764] [depth= 1] . ( 16 sec) [ -27357.8508] [ 5762] [depth= 4] . ( 16 sec) [ -27076.6241] [ 5761] [depth= 2] . ( 17 sec) [ -27058.1235] [ 5745] [depth= 3] . ( 17 sec) [ -27002.4406] [ 5746] [depth= 2] . ( 17 sec) [ -26980.3644] [ 5733] [depth= 9] . ( 17 sec) [ -26972.1225] [ 5729] [depth= 1] . ( 17 sec) [ -26971.5968] [ 5735] [depth= 1] . ( 18 sec) [ -26808.7120] [ 5691] [depth= 12] . ( 18 sec) [ -26734.7302] [ 5677] [depth= 20] . ( 18 sec) [ -26677.9344] [ 5666] [depth= 7] . ( 18 sec) [ -26585.0976] [ 5638] [depth= 14] . ( 19 sec) [ -26445.5649] [ 5624] [depth= 13] . ( 19 sec) [ -26427.9932] [ 5627] [depth= 1] . ( 19 sec) [ -26404.8805] [ 5621] [depth= 2] . ( 19 sec) [ -26389.7671] [ 5620] [depth= 1] . ( 19 sec) [ -26222.2292] [ 5563] [depth= 15] . ( 20 sec) [ -26175.9211] [ 5561] [depth= 1] . ( 20 sec) [ -26015.4199] [ 5516] [depth= 21] . ( 20 sec) [ -25996.4309] [ 5515] [depth= 1] . ( 20 sec) [ -25939.5350] [ 5505] [depth= 9] . ( 20 sec) [ -25933.8778] [ 5507] [depth= 1] . ( 21 sec) [ -25897.3813] [ 5499] [depth= 18] . ( 21 sec) [ -25892.4324] [ 5500] [depth= 3] . ( 21 sec) [ -25498.8717] [ 5373] [depth= 7] . ( 21 sec) [ -25255.1881] [ 5343] [depth= 14] . ( 22 sec) [ -25153.4656] [ 5304] [depth= 2] . ( 22 sec) [ -24782.9494] [ 5299] [depth= 14] . ( 22 sec) [ -24544.2346] [ 5288] [depth= 8] . ( 23 sec) [ -24475.0199] [ 5279] [depth= 10] . ( 23 sec) [ -24444.3082] [ 5274] [depth= 3] . ( 23 sec) [ -24435.0029] [ 5274] [depth= 1] . ( 23 sec) [ -24406.6552] [ 5271] [depth= 1] . ( 23 sec) [ -24332.7014] [ 5254] [depth= 8] . ( 24 sec) [ -24221.4913] [ 5234] [depth= 13] . ( 24 sec) [ -24218.6472] [ 5236] [depth= 1] . ( 24 sec) [ -23958.0490] [ 5073] [depth= 5] . ( 24 sec) [ -23850.4716] [ 5049] [depth= 14] . ( 25 sec) [ -23849.8925] [ 5049] [depth= 9] . ( 25 sec) [ -23818.8138] [ 5046] [depth= 7] . ( 25 sec) [ -23805.9640] [ 5046] [depth= 1] . ( 25 sec) [ -23728.3343] [ 5027] [depth= 15] . ( 25 sec) [ -23710.5768] [ 5023] [depth= 1] . ( 26 sec) [ -23497.0415] [ 5014] [depth= 5] . ( 26 sec) [ -23459.6821] [ 5003] [depth= 13] . ( 26 sec) [ -23370.3977] [ 4904] [depth= 6] . ( 26 sec) [ -23189.0775] [ 4897] [depth= 8] . ( 27 sec) [ -22962.4754] [ 4847] [depth= 9] . ( 27 sec) [ -22958.8600] [ 4849] [depth= 1] . ( 27 sec) [ -22947.2909] [ 4846] [depth= 1] . ( 27 sec) [ -22871.3247] [ 4786] [depth= 12] . ( 27 sec) [ -22778.8003] [ 4780] [depth= 1] . ( 28 sec) [ -22527.5094] [ 4702] [depth= 1] . ( 28 sec) [ -22492.3496] [ 4681] [depth= 1] . ( 28 sec) [ -22391.5381] [ 4666] [depth= 13] . ( 28 sec) [ -22364.2661] [ 4661] [depth= 1] . ( 29 sec) [ -22337.3488] [ 4655] [depth= 3] . ( 29 sec) [ -22285.2558] [ 4649] [depth= 3] . ( 29 sec) [ -22274.0732] [ 4654] [depth= 1] . ( 29 sec) [ -22169.0180] [ 4641] [depth= 4] . ( 30 sec) [ -22105.1887] [ 4645] [depth= 2] . ( 30 sec) [ -22028.4368] [ 4625] [depth= 3] . ( 30 sec) [ -22005.7209] [ 4593] [depth= 3] . ( 30 sec) [ -21959.1447] [ 4593] [depth= 5] . ( 31 sec) [ -21954.8078] [ 4586] [depth= 5] . ( 31 sec) [ -21935.1171] [ 4582] [depth= 2] . ( 31 sec) [ -21781.1050] [ 4536] [depth= 12] . ( 32 sec) [ -21709.6615] [ 4527] [depth= 2] . ( 32 sec) [ -21612.4204] [ 4503] [depth= 6] . ( 32 sec) [ -21535.4291] [ 4486] [depth= 7] . ( 32 sec) [ -21525.2870] [ 4471] [depth= 3] . ( 32 sec) [ -21461.3101] [ 4470] [depth= 1] . ( 33 sec) [ -21308.1202] [ 4425] [depth= 1] . ( 33 sec) [ -21298.3138] [ 4430] [depth= 1] . ( 33 sec) [ -21271.8558] [ 4440] [depth= 3] . ( 33 sec) [ -21114.7165] [ 4379] [depth= 16] . ( 33 sec) [ -21100.8417] [ 4379] [depth= 1] . ( 34 sec) [ -20874.4205] [ 4289] [depth= 10] . ( 34 sec) [ -20849.6251] [ 4284] [depth= 1] . ( 34 sec) [ -20760.9907] [ 4285] [depth= 1] . ( 34 sec) [ -20748.0882] [ 4284] [depth= 1] . ( 34 sec) [ -20721.3405] [ 4284] [depth= 1] . ( 35 sec) [ -20718.3903] [ 4280] [depth= 3] . ( 35 sec) [ -20713.7913] [ 4279] [depth= 1] . ( 35 sec) [ -20678.9190] [ 4282] [depth= 7] . ( 36 sec) [ -20630.9441] [ 4278] [depth= 2] . ( 36 sec) [ -20597.3554] [ 4269] [depth= 1] . ( 36 sec) [ -20561.8459] [ 4261] [depth= 2] . ( 36 sec) [ -20505.5770] [ 4242] [depth= 1] . ( 37 sec) [ -20463.8860] [ 4223] [depth= 11] . ( 37 sec) [ -20407.4915] [ 4204] [depth= 2] . ( 37 sec) [ -20393.5577] [ 4203] [depth= 14] . ( 37 sec) [ -19849.4386] [ 4198] [depth= 1] . ( 38 sec) [ -19541.0888] [ 4213] [depth= 2] . ( 38 sec) [ -19423.5748] [ 4080] [depth= 11] . ( 38 sec) [ -19419.6189] [ 4060] [depth= 9] . ( 38 sec) [ -19410.6885] [ 4054] [depth= 1] . ( 38 sec) [ -19374.2692] [ 4049] [depth= 11] . ( 39 sec) [ -19348.5611] [ 4051] [depth= 1] . ( 39 sec) [ -19338.0903] [ 4052] [depth= 1] . ( 39 sec) [ -19288.3653] [ 4038] [depth= 15] . ( 39 sec) [ -19210.6422] [ 4032] [depth= 10] . ( 40 sec) [ -19128.7516] [ 3982] [depth= 2] . ( 40 sec) [ -18990.5347] [ 3973] [depth= 8] . ( 40 sec) [ -18964.4193] [ 3970] [depth= 1] . ( 40 sec) [ -18921.8605] [ 3956] [depth= 1] . ( 40 sec) [ -18895.0388] [ 3955] [depth= 1] . ( 41 sec) [ -18873.3799] [ 3943] [depth= 6] . ( 41 sec) [ -18870.7697] [ 3944] [depth= 1] . ( 41 sec) [ -18869.7481] [ 3944] [depth= 1] . ( 41 sec) [ -18861.0555] [ 3942] [depth= 1] . ( 42 sec) [ -18768.1283] [ 3920] [depth= 4] . ( 42 sec) [ -18747.0108] [ 3915] [depth= 5] . ( 42 sec) [ -18714.5309] [ 3910] [depth= 6] . ( 42 sec) [ -18690.2510] [ 3904] [depth= 1] . ( 43 sec) [ -18653.1151] [ 3898] [depth= 7] . ( 43 sec) [ -18652.3409] [ 3898] [depth= 2] . ( 43 sec) [ -18647.5817] [ 3895] [depth= 3] . ( 43 sec) [ -18641.7292] [ 3893] [depth= 1] . ( 44 sec) [ -18641.1353] [ 3889] [depth= 5] . ( 44 sec) [ -18638.6144] [ 3887] [depth= 2] . ( 44 sec) [ -18631.8191] [ 3888] [depth= 1] . ( 44 sec) [ -18604.1279] [ 3878] [depth= 1] . ( 44 sec) [ -18600.9196] [ 3878] [depth= 1] . ( 44 sec) [ -18597.8956] [ 3878] [depth= 1] . ( 45 sec) [ -18573.5126] [ 3874] [depth= 6] . ( 45 sec) [ -18569.5325] [ 3874] [depth= 1] . ( 45 sec) [ -18566.8952] [ 3871] [depth= 1] . ( 46 sec) [ -18530.2251] [ 3871] [depth= 14] . ( 46 sec) [ -18286.5174] [ 3820] [depth= 12] . ( 46 sec) [ -18284.6640] [ 3819] [depth= 3] . ( 46 sec) [ -18222.3471] [ 3827] [depth= 1] . ( 47 sec) [ -18173.3880] [ 3810] [depth= 10] . ( 47 sec) [ -18167.0633] [ 3808] [depth= 3] . ( 47 sec) [ -18164.1721] [ 3807] [depth= 4] . ( 47 sec) [ -18128.2416] [ 3800] [depth= 7] . ( 48 sec) [ -18126.3458] [ 3799] [depth= 3] . ( 48 sec) [ -18118.8171] [ 3794] [depth= 2] . ( 48 sec) [ -18105.3459] [ 3793] [depth= 1] . ( 48 sec) [ -17935.4063] [ 3785] [depth= 1] . ( 48 sec) [ -17786.7464] [ 3730] [depth= 8] . ( 49 sec) [ -17487.4415] [ 3735] [depth= 8] . ( 49 sec) [ -17461.0863] [ 3733] [depth= 1] . ( 49 sec) [ -17352.9934] [ 3694] [depth= 9] . ( 50 sec) [ -17335.3071] [ 3687] [depth= 1] . ( 50 sec) [ -17298.1716] [ 3674] [depth= 1] . ( 50 sec) [ -17275.4821] [ 3677] [depth= 2] . ( 50 sec) [ -17251.1107] [ 3674] [depth= 2] . ( 51 sec) [ -17167.2467] [ 3645] [depth= 1] . ( 51 sec) [ -17141.3028] [ 3637] [depth= 1] . ( 51 sec) [ -17139.1361] [ 3637] [depth= 1] . ( 52 sec) [ -17130.6916] [ 3635] [depth= 2] . ( 52 sec) [ -17052.8112] [ 3608] [depth= 5] . ( 52 sec) [ -17026.4857] [ 3612] [depth= 1] . ( 52 sec) [ -17025.4333] [ 3615] [depth= 1] . ( 53 sec) [ -16990.8941] [ 3594] [depth= 1] . ( 53 sec) [ -16980.1833] [ 3600] [depth= 1] . ( 53 sec) [ -16955.0956] [ 3579] [depth= 2] . ( 53 sec) [ -16954.5970] [ 3582] [depth= 1] . ( 53 sec) [ -16951.8800] [ 3581] [depth= 3] . ( 54 sec) [ -16944.7128] [ 3579] [depth= 5] . ( 54 sec) [ -16943.6011] [ 3579] [depth= 1] . ( 55 sec) [ -16943.2288] [ 3581] [depth= 2] . ( 55 sec) [ -16942.7153] [ 3588] [depth= 1] . ( 55 sec) [ -16874.2716] [ 3590] [depth= 1] . ( 55 sec) [ -16863.4362] [ 3589] [depth= 4] . ( 56 sec) [ -16862.9908] [ 3591] [depth= 3] . ( 56 sec) [ -16861.8271] [ 3592] [depth= 1] . ( 56 sec) [ -16858.8912] [ 3590] [depth= 3] . ( 57 sec) [ -16826.5114] [ 3589] [depth= 2] . ( 57 sec) [ -16821.6079] [ 3585] [depth= 1] . ( 57 sec) [ -16786.3295] [ 3575] [depth= 2] . ( 57 sec) [ -16782.8346] [ 3578] [depth= 2] . ( 58 sec) [ -16781.2337] [ 3581] [depth= 3] . ( 59 sec) [ -16350.8602] [Branch lengths ] . ( 67 sec) [ -16317.7805] [GTR parameters ] . ( 68 sec) [ -16317.6772] [Alpha ][ 0.491563] . ( 68 sec) [ -16314.3429] [ 3575] [depth= 1] . ( 69 sec) [ -16307.9278] [ 3571] [depth= 2] . ( 69 sec) [ -16298.5476] [ 3567] [depth= 1] . ( 69 sec) [ -16298.3581] [ 3567] [depth= 1] . ( 71 sec) [ -16297.9333] [ 3568] [depth= 3] . ( 72 sec) [ -16297.7270] [ 3568] [depth= 1] . ( 72 sec) [ -16296.2464] [ 3567] [depth= 2] . ( 72 sec) [ -16231.0438] [ 3539] [depth= 5] . ( 72 sec) [ -16218.9419] [ 3536] [depth= 1] . ( 74 sec) [ -16181.8350] [ 3515] [depth= 11] . ( 74 sec) [ -16175.4467] [ 3511] [depth= 1] . ( 74 sec) [ -16170.0614] [ 3510] [depth= 1] . ( 75 sec) [ -16169.2502] [ 3508] [depth= 2] . ( 75 sec) [ -16118.8521] [ 3489] [depth= 10] . ( 76 sec) [ -16115.4804] [ 3451] [depth= 2] . ( 76 sec) [ -16108.4233] [ 3447] [depth= 4] . ( 76 sec) [ -16107.2544] [ 3446] [depth= 3] . ( 76 sec) [ -16081.9342] [ 3436] [depth= 7] . ( 76 sec) [ -16080.8132] [ 3435] [depth= 2] . ( 77 sec) [ -16080.5561] [ 3435] [depth= 1] . ( 78 sec) [ -16078.2101] [ 3440] [depth= 1] . ( 78 sec) [ -16070.9761] [ 3442] [depth= 7] . ( 79 sec) [ -16060.1342] [ 3432] [depth= 1] . ( 79 sec) [ -16058.4627] [ 3430] [depth= 1] . ( 79 sec) [ -16052.9817] [ 3430] [depth= 2] . ( 80 sec) [ -16052.9158] [ 3430] [depth= 2] . ( 80 sec) [ -16051.1195] [ 3409] [depth= 13] . ( 81 sec) [ -16049.9006] [ 3417] [depth= 1] . ( 81 sec) [ -16041.9123] [ 3412] [depth= 1] . ( 81 sec) [ -16040.2891] [ 3411] [depth= 1] . ( 83 sec) [ -16038.8774] [ 3410] [depth= 1] . ( 83 sec) [ -16036.5963] [ 3409] [depth= 2] . ( 84 sec) [ -16036.3562] [ 3409] [depth= 1] . ( 84 sec) [ -16036.0239] [ 3410] [depth= 1] . ( 84 sec) [ -16035.8645] [ 3411] [depth= 1] . ( 85 sec) [ -16034.0951] [ 3410] [depth= 1] . ( 86 sec) [ -15991.2118] [ 3335] [depth= 6] . ( 86 sec) [ -15989.9497] [ 3337] [depth= 2] . ( 86 sec) [ -15989.5924] [ 3337] [depth= 1] . ( 88 sec) [ -15988.6077] [ 3346] [depth= 1] . ( 88 sec) [ -15943.6021] [ 3334] [depth= 2] . ( 90 sec) [ -15942.4227] [ 3333] [depth= 1] . ( 90 sec) [ -15935.8619] [ 3315] [depth= 10] . ( 91 sec) [ -15930.3709] [ 3291] [depth= 14] . ( 93 sec) [ -15930.2870] [ 3291] [depth= 1] . ( 93 sec) [ -15923.2467] [ 3291] [depth= 1] . ( 94 sec) [ -15880.2216] [ 3293] [depth= 10] . ( 95 sec) [ -15879.0235] [ 3295] [depth= 1] . ( 95 sec) [ -15863.5355] [ 3290] [depth= 1] . ( 96 sec) [ -15861.8583] [ 3290] [depth= 2] . ( 96 sec) [ -15860.0657] [ 3286] [depth= 1] . ( 96 sec) [ -15845.0431] [ 3283] [depth= 1] . ( 97 sec) [ -15829.2215] [ 3281] [depth= 1] . ( 97 sec) [ -15826.9560] [ 3280] [depth= 2] . ( 98 sec) [ -15826.3549] [ 3278] [depth= 1] . ( 99 sec) [ -15825.5419] [ 3276] [depth= 1] . ( 99 sec) [ -15818.2291] [ 3270] [depth= 1] . ( 101 sec) [ -15817.9150] [ 3270] [depth= 1] . ( 103 sec) [ -15815.4770] [ 3270] [depth= 1] . ( 104 sec) [ -15815.3613] [ 3270] [depth= 1] . ( 107 sec) [ -15813.9833] [ 3270] [depth= 1] . ( 107 sec) [ -15813.9280] [ 3270] [depth= 1] . ( 109 sec) [ -15811.7300] [ 3268] [depth= 1] . ( 110 sec) [ -15811.3622] [ 3269] [depth= 3] . ( 110 sec) [ -15811.2663] [ 3268] [depth= 1] . ( 111 sec) [ -15810.8922] [ 3268] [depth= 1] . ( 112 sec) [ -15809.9615] [ 3268] [depth= 1] . ( 113 sec) [ -15793.8380] [ 3270] [depth= 1] . ( 113 sec) [ -15793.2714] [ 3271] [depth= 1] . ( 113 sec) [ -15786.8420] [ 3272] [depth= 2] . ( 115 sec) [ -15786.4203] [ 3272] [depth= 2] . ( 121 sec) [ -15785.4643] [ 3269] [depth= 1] . ( 123 sec) [ -15742.8660] [Branch lengths ] . ( 129 sec) [ -15742.1956] [GTR parameters ] . ( 129 sec) [ -15741.0124] [Alpha ][ 0.527081] . ( 129 sec) [ -15739.2740] [ 3267] [depth= 1] . ( 137 sec) [ -15739.2024] [ 3255] [depth= 1] . ( 138 sec) [ -15735.5631] [ 3245] [depth= 6] . ( 145 sec) [ -15730.5043] [ 3216] [depth= 5] . ( 145 sec) [ -15730.4507] [ 3217] [depth= 1] . ( 146 sec) [ -15730.4105] [ 3217] [depth= 1] . ( 156 sec) [ -15728.7349] [ 3217] [depth= 1] . ( 157 sec) [ -15691.5299] [ 3198] [depth= 1] . ( 170 sec) [ -15690.8255] [ 3199] [depth= 1] . ( 176 sec) [ -15690.7548] [ 3198] [depth= 1] . ( 179 sec) [ -15690.7002] [ 3199] [depth= 1] . ( 188 sec) [ -15690.2388] [ 3199] [depth= 1] . ( 190 sec) [ -15671.1589] [Branch lengths ] . ( 193 sec) [ -15671.0117] [GTR parameters ] . ( 193 sec) [ -15670.8061] [Alpha ][ 0.542804] . ( 194 sec) [ -15667.8153] [ 3198] [depth= 1] . ( 253 sec) [ -15665.6907] [Branch lengths ] . ( 257 sec) [ -15665.6799] [GTR parameters ] . ( 257 sec) [ -15665.6786] [Alpha ][ 0.544044] . ( 314 sec) [ -15664.7430] [Branch lengths ] . ( 474 sec) [ -15664.1739] [Branch lengths ] . ( 474 sec) [ -15664.1739] [Topology ] . ( 478 sec) [ -15663.8748] [Topology ] . ( 481 sec) [ -15662.6360] [Topology ] . ( 485 sec) [ -15660.0285] [Topology ] . ( 489 sec) [ -15659.4399] [Topology ] . ( 493 sec) [ -15659.3412] [Topology ] . ( 497 sec) [ -15659.3206] [Topology ] . ( 499 sec) [ -15659.3171] [GTR parameters ] . ( 499 sec) [ -15659.3118] [Alpha ][ 0.546664] . ( 499 sec) [ -15659.3118] [Topology ] . ( 503 sec) [ -15659.3047] [Topology ] . ( 506 sec) [ -15659.3010] [Topology ] . ( 510 sec) [ -15659.2984] [Topology ] . ( 514 sec) [ -15659.2964] [Topology ] . ( 517 sec) [ -15659.2946] [Topology ] . ( 521 sec) [ -15659.2930] [Topology ] . ( 522 sec) [ -15659.2929] [GTR parameters ] . ( 522 sec) [ -15659.2929] [Alpha ][ 0.546664] . ( 522 sec) [ -15659.2929] [Topology ] . ( 526 sec) [ -15659.2912] [Topology ] . ( 530 sec) [ -15659.2896] [Topology ] . ( 534 sec) [ -15659.2879] [Topology ] . ( 538 sec) [ -15659.2871] [Topology ] . ( 538 sec) [ -15659.2871] [GTR parameters ] . ( 539 sec) [ -15659.2871] [Alpha ][ 0.546664] . ( 539 sec) [ -15659.2871] [Topology ] . ( 542 sec) [ -15659.2869] [Topology ] . ( 543 sec) [ -15659.2869] [GTR parameters ] . ( 543 sec) [ -15659.2869] [Alpha ][ 0.546664] . Checking for NNIs, optimizing five branches... . ( 572 sec) [ -15659.2809] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15659.280925. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 6 sec) [ -16171.4937] [GTR parameters ] . ( 7 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 7 sec) [ -16055.6228] [Topology ] . ( 11 sec) [ -15746.4015] [Topology ] . ( 15 sec) [ -15704.7329] [Topology ] . ( 19 sec) [ -15695.3163] [Topology ] . ( 23 sec) [ -15693.0363] [Topology ] . ( 28 sec) [ -15692.2250] [Topology ] . ( 32 sec) [ -15691.7236] [Topology ] . ( 36 sec) [ -15691.0034] [Topology ] . ( 39 sec) [ -15689.1725] [Topology ] . ( 43 sec) [ -15687.5621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 72 sec) [ -15687.0077] [Topology ] . ( 80 sec) [ -15674.2751] [GTR parameters ] . ( 81 sec) [ -15673.3524] [Alpha ][ 0.534838] . ( 81 sec) [ -15673.3524] [Topology ] . ( 85 sec) [ -15671.9309] [Topology ] . ( 89 sec) [ -15671.3290] [Topology ] . ( 93 sec) [ -15670.9763] [Topology ] . ( 97 sec) [ -15670.7498] [Topology ] . ( 100 sec) [ -15670.5983] [Topology ] . ( 104 sec) [ -15670.4943] [Topology ] . Checking for NNIs, optimizing five branches... . ( 132 sec) [ -15670.4657] [Topology ] . ( 138 sec) [ -15670.3857] [GTR parameters ] . ( 138 sec) [ -15670.3285] [Alpha ][ 0.543674] . ( 138 sec) [ -15670.3285] [Topology ] . ( 142 sec) [ -15670.1641] [Topology ] . ( 146 sec) [ -15670.0851] [Topology ] . ( 150 sec) [ -15670.0324] [Topology ] . ( 153 sec) [ -15669.9950] [Topology ] . ( 157 sec) [ -15669.9680] [Topology ] . ( 160 sec) [ -15669.9482] [Topology ] . Checking for NNIs, optimizing five branches... . ( 188 sec) [ -15669.9480] [Topology ] . ( 191 sec) [ -15669.9440] [GTR parameters ] . ( 191 sec) [ -15669.9395] [Alpha ][ 0.546104] . ( 191 sec) [ -15669.9395] [Topology ] . ( 195 sec) [ -15669.9214] [Topology ] . ( 199 sec) [ -15669.9081] [Topology ] . ( 203 sec) [ -15669.8982] [Topology ] . ( 206 sec) [ -15669.8909] [Topology ] . ( 210 sec) [ -15669.8854] [Topology ] . ( 214 sec) [ -15669.8813] [Topology ] . Checking for NNIs, optimizing five branches... . ( 243 sec) [ -15669.8803] [GTR parameters ] . ( 243 sec) [ -15669.8797] [Alpha ][ 0.547002] . ( 243 sec) [ -15669.8797] [Topology ] . ( 247 sec) [ -15669.8759] [Topology ] . ( 250 sec) [ -15669.8731] [Topology ] . ( 254 sec) [ -15669.8710] [Topology ] . ( 258 sec) [ -15669.8694] [Topology ] . ( 261 sec) [ -15669.8681] [Topology ] . ( 265 sec) [ -15669.8672] [Topology ] . Checking for NNIs, optimizing five branches... . ( 297 sec) [ -15669.8667] [GTR parameters ] . ( 297 sec) [ -15669.8666] [Alpha ][ 0.547549] . ( 298 sec) [ -15669.8666] [Topology ] . ( 302 sec) [ -15669.8657] [Topology ] . Checking for NNIs, optimizing five branches... . ( 331 sec) [ -15669.8657] [GTR parameters ] . ( 331 sec) [ -15669.8657] [Alpha ][ 0.547549] . ( 331 sec) [ -15669.8657] [Topology ] . ( 335 sec) [ -15669.8650] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 394 sec) [ -16171.4937] [GTR parameters ] . ( 394 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 395 sec) [ -16051.9734] [ 3233] [depth= 1] . ( 395 sec) [ -16044.4728] [ 3239] [depth= 1] . ( 395 sec) [ -16041.2101] [ 3233] [depth= 1] . ( 395 sec) [ -16031.8120] [ 3236] [depth= 1] . ( 396 sec) [ -16011.4895] [ 3239] [depth= 2] . ( 396 sec) [ -16011.3510] [ 3251] [depth= 2] . ( 397 sec) [ -16002.2772] [ 3253] [depth= 1] . ( 397 sec) [ -15994.3577] [ 3257] [depth= 2] . ( 397 sec) [ -15992.1697] [ 3252] [depth= 2] . ( 397 sec) [ -15990.1296] [ 3256] [depth= 1] . ( 398 sec) [ -15986.2747] [ 3253] [depth= 1] . ( 398 sec) [ -15977.1070] [ 3251] [depth= 1] . ( 399 sec) [ -15973.2771] [ 3237] [depth= 1] . ( 399 sec) [ -15962.2787] [ 3234] [depth= 1] . ( 399 sec) [ -15961.2844] [ 3238] [depth= 1] . ( 400 sec) [ -15934.6332] [ 3238] [depth= 1] . ( 400 sec) [ -15926.3319] [ 3233] [depth= 1] . ( 400 sec) [ -15926.1471] [ 3237] [depth= 2] . ( 400 sec) [ -15894.8668] [ 3228] [depth= 4] . ( 401 sec) [ -15891.4821] [ 3232] [depth= 1] . ( 401 sec) [ -15890.0526] [ 3234] [depth= 2] . ( 401 sec) [ -15888.1122] [ 3228] [depth= 1] . ( 402 sec) [ -15869.6602] [ 3219] [depth= 1] . ( 402 sec) [ -15868.3150] [ 3222] [depth= 1] . ( 402 sec) [ -15859.4357] [ 3218] [depth= 1] . ( 403 sec) [ -15857.6811] [ 3213] [depth= 1] . ( 403 sec) [ -15856.8559] [ 3212] [depth= 1] . ( 403 sec) [ -15850.7281] [ 3215] [depth= 2] . ( 403 sec) [ -15850.6540] [ 3215] [depth= 1] . ( 404 sec) [ -15848.4548] [ 3213] [depth= 3] . ( 404 sec) [ -15847.6184] [ 3213] [depth= 3] . ( 405 sec) [ -15842.3468] [ 3212] [depth= 3] . ( 405 sec) [ -15840.1403] [ 3211] [depth= 1] . ( 405 sec) [ -15838.9389] [ 3211] [depth= 1] . ( 406 sec) [ -15838.9216] [ 3213] [depth= 1] . ( 406 sec) [ -15837.5423] [ 3211] [depth= 2] . ( 406 sec) [ -15836.2600] [ 3210] [depth= 1] . ( 408 sec) [ -15835.9759] [ 3211] [depth= 1] . ( 409 sec) [ -15832.9401] [ 3210] [depth= 1] . ( 410 sec) [ -15829.5869] [ 3210] [depth= 1] . ( 414 sec) [ -15829.1001] [ 3207] [depth= 1] . ( 415 sec) [ -15828.0095] [ 3209] [depth= 1] . ( 415 sec) [ -15825.9446] [ 3209] [depth= 1] . ( 416 sec) [ -15824.7571] [ 3209] [depth= 1] . ( 416 sec) [ -15819.9096] [ 3210] [depth= 1] . ( 417 sec) [ -15819.3978] [ 3210] [depth= 1] . ( 418 sec) [ -15818.9106] [ 3210] [depth= 1] . ( 418 sec) [ -15810.4986] [ 3210] [depth= 1] . ( 418 sec) [ -15810.0893] [ 3209] [depth= 1] . ( 419 sec) [ -15809.8308] [ 3209] [depth= 1] . ( 420 sec) [ -15809.6352] [ 3211] [depth= 1] . ( 421 sec) [ -15809.1639] [ 3211] [depth= 1] . ( 421 sec) [ -15809.0293] [ 3208] [depth= 1] . ( 421 sec) [ -15808.8563] [ 3207] [depth= 1] . ( 424 sec) [ -15805.7668] [ 3206] [depth= 1] . ( 424 sec) [ -15804.8210] [ 3206] [depth= 1] . ( 424 sec) [ -15804.2174] [ 3206] [depth= 1] . ( 425 sec) [ -15803.8278] [ 3206] [depth= 1] . ( 426 sec) [ -15803.3799] [ 3207] [depth= 3] . ( 426 sec) [ -15802.1832] [ 3207] [depth= 1] . ( 426 sec) [ -15802.0612] [ 3207] [depth= 1] . ( 427 sec) [ -15801.8047] [ 3208] [depth= 1] . ( 429 sec) [ -15801.6389] [ 3207] [depth= 3] . ( 430 sec) [ -15801.0621] [ 3207] [depth= 2] . ( 431 sec) [ -15799.8267] [ 3207] [depth= 1] . ( 432 sec) [ -15796.3603] [ 3208] [depth= 2] . ( 432 sec) [ -15795.9391] [ 3208] [depth= 1] . ( 433 sec) [ -15795.8642] [ 3208] [depth= 1] . ( 433 sec) [ -15795.5001] [ 3208] [depth= 1] . ( 434 sec) [ -15795.4702] [ 3208] [depth= 1] . ( 436 sec) [ -15794.4144] [ 3208] [depth= 1] . ( 438 sec) [ -15793.6256] [ 3208] [depth= 1] . ( 439 sec) [ -15793.4448] [ 3208] [depth= 1] . ( 440 sec) [ -15793.4310] [ 3208] [depth= 1] . ( 441 sec) [ -15793.3560] [ 3208] [depth= 1] . ( 441 sec) [ -15793.2598] [ 3208] [depth= 1] . ( 442 sec) [ -15793.2068] [ 3208] [depth= 1] . ( 444 sec) [ -15701.4518] [Branch lengths ] . ( 452 sec) [ -15691.2786] [GTR parameters ] . ( 453 sec) [ -15690.6608] [Alpha ][ 0.528636] . ( 454 sec) [ -15688.7715] [ 3205] [depth= 1] . ( 454 sec) [ -15688.3912] [ 3205] [depth= 1] . ( 455 sec) [ -15687.6891] [ 3208] [depth= 1] . ( 457 sec) [ -15686.9522] [ 3208] [depth= 1] . ( 457 sec) [ -15685.9380] [ 3206] [depth= 1] . ( 460 sec) [ -15685.3836] [ 3208] [depth= 1] . ( 461 sec) [ -15683.1610] [ 3202] [depth= 2] . ( 462 sec) [ -15682.8318] [ 3203] [depth= 1] . ( 466 sec) [ -15682.6232] [ 3202] [depth= 1] . ( 499 sec) [ -15682.5115] [ 3202] [depth= 1] . ( 510 sec) [ -15668.2499] [Branch lengths ] . ( 514 sec) [ -15668.0859] [GTR parameters ] . ( 515 sec) [ -15668.0175] [Alpha ][ 0.538332] . ( 521 sec) [ -15667.9356] [ 3201] [depth= 1] . ( 574 sec) [ -15665.9925] [Branch lengths ] . ( 578 sec) [ -15665.9523] [GTR parameters ] . ( 578 sec) [ -15665.9522] [Alpha ][ 0.538870] . ( 637 sec) [ -15665.2221] [Branch lengths ] . ( 666 sec) [ -15665.2018] [ 3198] [depth= 1] . ( 788 sec) [ -15665.1883] [ 3198] [depth= 2] . ( 794 sec) [ -15664.4440] [Branch lengths ] . ( 799 sec) [ -15664.4289] [GTR parameters ] . ( 799 sec) [ -15664.4139] [Alpha ][ 0.543379] . ( 799 sec) [ -15664.4139] [Topology ] . ( 803 sec) [ -15664.0797] [Topology ] . ( 806 sec) [ -15662.9541] [Topology ] . ( 810 sec) [ -15660.9366] [Topology ] . ( 813 sec) [ -15660.5195] [Topology ] . ( 817 sec) [ -15660.4558] [Topology ] . ( 821 sec) [ -15660.4338] [Topology ] . ( 824 sec) [ -15660.4330] [GTR parameters ] . ( 825 sec) [ -15660.4301] [Alpha ][ 0.545315] . ( 825 sec) [ -15660.4301] [Topology ] . ( 828 sec) [ -15660.4171] [Topology ] . ( 832 sec) [ -15660.4087] [Topology ] . ( 836 sec) [ -15660.4028] [Topology ] . ( 839 sec) [ -15660.3985] [Topology ] . ( 843 sec) [ -15660.3953] [Topology ] . ( 847 sec) [ -15660.3930] [Topology ] . ( 848 sec) [ -15660.3925] [GTR parameters ] . ( 849 sec) [ -15660.3922] [Alpha ][ 0.545936] . ( 849 sec) [ -15660.3922] [Topology ] . ( 852 sec) [ -15660.3902] [Topology ] . ( 856 sec) [ -15660.3886] [Topology ] . ( 859 sec) [ -15660.3875] [Topology ] . ( 863 sec) [ -15660.3867] [Topology ] . ( 864 sec) [ -15660.3866] [GTR parameters ] . ( 865 sec) [ -15660.3866] [Alpha ][ 0.545936] . ( 865 sec) [ -15660.3866] [Topology ] . ( 868 sec) [ -15660.3859] [Topology ] . ( 869 sec) [ -15660.3858] [GTR parameters ] . ( 870 sec) [ -15660.3858] [Alpha ][ 0.545936] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -15669.865032 . Log likelihood obtained after SPR moves : -15660.385831 . Log likelihood of the current tree: -15660.385831. . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Best log likelihood : -15658.535132 . Time used 0h14m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3618.98user 0.00system 1:02:15elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps