.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M4055_306x7062_2008.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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 65 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 6303 patterns found. (out of a total of 7062 sites) . 703 sites without polymorphism (9.95%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1028Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 113 sec) [ -298394.7746] [GTR parameters ] . ( 124 sec) [ -298078.9669] [Alpha ][ 0.712583] . ( 137 sec) [ -298025.8027] [81814] [depth= 1] . ( 143 sec) [ -297994.9293] [81795] [depth= 1] . ( 172 sec) [ -297959.4066] [81776] [depth= 2] . ( 195 sec) [ -297957.7556] [81780] [depth= 1] . ( 201 sec) [ -297930.7567] [81778] [depth= 1] . ( 213 sec) [ -297921.2314] [81783] [depth= 1] . ( 220 sec) [ -297674.0442] [81666] [depth= 36] . ( 225 sec) [ -297654.4251] [81668] [depth= 1] . ( 234 sec) [ -297652.9955] [81667] [depth= 1] . ( 239 sec) [ -297642.8590] [81668] [depth= 1] . ( 244 sec) [ -297604.2625] [81618] [depth= 7] . ( 257 sec) [ -297600.6625] [81614] [depth= 1] . ( 262 sec) [ -297557.9756] [81589] [depth= 4] . ( 265 sec) [ -297557.1053] [81587] [depth= 1] . ( 270 sec) [ -297529.0903] [81586] [depth= 1] . ( 278 sec) [ -297476.3883] [81554] [depth= 3] . ( 285 sec) [ -297395.6664] [81539] [depth= 7] . ( 290 sec) [ -297124.6277] [81179] [depth= 38] . ( 300 sec) [ -297104.1864] [81170] [depth= 2] . ( 316 sec) [ -297102.6227] [81161] [depth= 2] . ( 321 sec) [ -296998.5013] [81086] [depth= 9] . ( 330 sec) [ -296993.7658] [81090] [depth= 8] . ( 335 sec) [ -296938.0282] [81055] [depth= 25] . ( 340 sec) [ -296933.0005] [81055] [depth= 2] . ( 350 sec) [ -296783.8843] [80957] [depth= 21] . ( 357 sec) [ -296773.6135] [80945] [depth= 1] . ( 362 sec) [ -296769.1593] [80950] [depth= 5] . ( 368 sec) [ -296768.6804] [80954] [depth= 17] . ( 375 sec) [ -296720.6580] [80908] [depth= 5] . ( 383 sec) [ -296718.9530] [80885] [depth= 10] . ( 389 sec) [ -296700.0441] [80869] [depth= 1] . ( 403 sec) [ -296688.5675] [80859] [depth= 5] . ( 408 sec) [ -296611.1198] [80817] [depth= 16] . ( 416 sec) [ -296586.7948] [80821] [depth= 1] . ( 426 sec) [ -296521.1104] [80793] [depth= 15] . ( 431 sec) [ -296278.9591] [80789] [depth= 1] . ( 436 sec) [ -296120.9231] [80744] [depth= 10] . ( 441 sec) [ -296084.4247] [80722] [depth= 4] . ( 447 sec) [ -296078.8031] [80724] [depth= 3] . ( 452 sec) [ -296055.7336] [80714] [depth= 6] . ( 457 sec) [ -296013.8186] [80691] [depth= 3] . ( 465 sec) [ -295990.2334] [80694] [depth= 1] . ( 470 sec) [ -295983.5495] [80692] [depth= 2] . ( 476 sec) [ -295962.5022] [80678] [depth= 3] . ( 483 sec) [ -295961.0118] [80664] [depth= 1] . ( 490 sec) [ -295943.1332] [80651] [depth= 2] . ( 495 sec) [ -295941.9276] [80646] [depth= 1] . ( 501 sec) [ -295896.6696] [80629] [depth= 2] . ( 506 sec) [ -295883.9863] [80616] [depth= 4] . ( 511 sec) [ -295880.2174] [80617] [depth= 1] . ( 517 sec) [ -295878.9393] [80622] [depth= 1] . ( 531 sec) [ -295833.6574] [80605] [depth= 16] . ( 536 sec) [ -295809.2146] [80593] [depth= 15] . ( 541 sec) [ -295790.5729] [80590] [depth= 7] . ( 546 sec) [ -295765.9049] [80578] [depth= 2] . ( 551 sec) [ -295762.7762] [80570] [depth= 2] . ( 556 sec) [ -295718.1806] [80573] [depth= 7] . ( 562 sec) [ -295475.9263] [80448] [depth= 38] . ( 567 sec) [ -295409.5455] [80409] [depth= 15] . ( 572 sec) [ -295325.7239] [80385] [depth= 6] . ( 593 sec) [ -295324.7542] [80390] [depth= 1] . ( 599 sec) [ -295305.2536] [80376] [depth= 3] . ( 604 sec) [ -295298.7854] [80367] [depth= 3] . ( 611 sec) [ -295297.5150] [80387] [depth= 3] . ( 616 sec) [ -295286.3196] [80374] [depth= 3] . ( 621 sec) [ -295277.1913] [80377] [depth= 1] . ( 626 sec) [ -295136.4990] [80314] [depth= 5] . ( 631 sec) [ -295133.8190] [80319] [depth= 1] . ( 637 sec) [ -295024.8404] [80270] [depth= 17] . ( 642 sec) [ -294960.9562] [80227] [depth= 19] . ( 647 sec) [ -294935.1705] [80206] [depth= 8] . ( 661 sec) [ -294914.5550] [80164] [depth= 6] . ( 667 sec) [ -294910.7075] [80166] [depth= 6] . ( 681 sec) [ -294909.4198] [80169] [depth= 1] . ( 686 sec) [ -294902.4710] [80159] [depth= 1] . ( 691 sec) [ -294902.4282] [80159] [depth= 1] . ( 697 sec) [ -294901.5366] [80154] [depth= 1] . ( 702 sec) [ -294897.6945] [80101] [depth= 22] . ( 708 sec) [ -294871.8904] [80086] [depth= 3] . ( 714 sec) [ -294871.6621] [80076] [depth= 1] . ( 730 sec) [ -294869.4240] [80072] [depth= 1] . ( 735 sec) [ -294828.1753] [80052] [depth= 9] . ( 741 sec) [ -294818.2095] [80043] [depth= 1] . ( 748 sec) [ -294768.5849] [80029] [depth= 11] . ( 758 sec) [ -294767.9496] [80039] [depth= 1] . ( 766 sec) [ -294749.0385] [80043] [depth= 3] . ( 779 sec) [ -294700.9802] [80023] [depth= 15] . ( 784 sec) [ -294662.7061] [80013] [depth= 3] . ( 789 sec) [ -294540.2999] [79975] [depth= 6] . ( 795 sec) [ -294530.4743] [79965] [depth= 3] . ( 800 sec) [ -294449.4300] [79908] [depth= 8] . ( 817 sec) [ -294440.8021] [79911] [depth= 1] . ( 825 sec) [ -294425.5757] [79888] [depth= 2] . ( 829 sec) [ -294386.4339] [79854] [depth= 1] . ( 837 sec) [ -294376.4282] [79854] [depth= 1] . ( 842 sec) [ -294364.7572] [79854] [depth= 1] . ( 848 sec) [ -294362.8864] [79858] [depth= 1] . ( 854 sec) [ -294358.7595] [79853] [depth= 1] . ( 859 sec) [ -294346.2690] [79838] [depth= 2] . ( 865 sec) [ -294342.3453] [79792] [depth= 28] . ( 870 sec) [ -294323.4458] [79773] [depth= 4] . ( 878 sec) [ -294319.7337] [79773] [depth= 1] . ( 881 sec) [ -294298.9261] [79780] [depth= 1] . ( 886 sec) [ -294282.1037] [79772] [depth= 5] . ( 892 sec) [ -294248.2455] [79787] [depth= 1] . ( 897 sec) [ -294168.7067] [79760] [depth= 10] . ( 902 sec) [ -294163.5963] [79749] [depth= 1] . ( 909 sec) [ -293997.5387] [79707] [depth= 24] . ( 914 sec) [ -293973.1494] [79701] [depth= 3] . ( 924 sec) [ -293970.8009] [79705] [depth= 1] . ( 929 sec) [ -293940.1430] [79688] [depth= 7] . ( 935 sec) [ -293938.2021] [79680] [depth= 4] . ( 940 sec) [ -293929.5008] [79656] [depth= 8] . ( 945 sec) [ -293865.9851] [79600] [depth= 11] . ( 950 sec) [ -293863.6253] [79598] [depth= 3] . ( 956 sec) [ -293728.3747] [79603] [depth= 1] . ( 961 sec) [ -293725.8364] [79599] [depth= 4] . ( 969 sec) [ -293714.3888] [79609] [depth= 2] . ( 974 sec) [ -293708.3656] [79612] [depth= 1] . ( 989 sec) [ -293697.5861] [79608] [depth= 2] . ( 994 sec) [ -293673.3252] [79581] [depth= 17] . ( 1008 sec) [ -293657.8083] [79565] [depth= 1] . ( 1020 sec) [ -293623.8062] [79554] [depth= 3] . ( 1025 sec) [ -293474.7550] [79479] [depth= 19] . ( 1030 sec) [ -293389.8556] [79469] [depth= 1] . ( 1035 sec) [ -293383.5161] [79468] [depth= 1] . ( 1041 sec) [ -293372.3764] [79473] [depth= 1] . ( 1047 sec) [ -293330.7375] [79434] [depth= 3] . ( 1053 sec) [ -293316.2180] [79436] [depth= 2] . ( 1058 sec) [ -293316.0134] [79438] [depth= 1] . ( 1068 sec) [ -293290.7205] [79436] [depth= 2] . ( 1075 sec) [ -293290.6807] [79411] [depth= 2] . ( 1085 sec) [ -293173.1658] [79356] [depth= 13] . ( 1090 sec) [ -293151.7580] [79339] [depth= 13] . ( 1100 sec) [ -293149.7443] [79336] [depth= 4] . ( 1106 sec) [ -293146.6964] [79341] [depth= 1] . ( 1109 sec) [ -293144.7207] [79330] [depth= 1] . ( 1114 sec) [ -293137.3341] [79328] [depth= 1] . ( 1118 sec) [ -293132.3723] [79327] [depth= 2] . ( 1123 sec) [ -293049.2763] [79331] [depth= 2] . ( 1134 sec) [ -293031.7975] [79328] [depth= 10] . ( 1139 sec) [ -293028.7010] [79332] [depth= 1] . ( 1145 sec) [ -293023.1618] [79333] [depth= 1] . ( 1150 sec) [ -292851.6679] [79257] [depth= 11] . ( 1155 sec) [ -292831.2236] [79244] [depth= 2] . ( 1163 sec) [ -292822.9553] [79246] [depth= 1] . ( 1168 sec) [ -292810.1286] [79240] [depth= 3] . ( 1173 sec) [ -292773.5095] [79224] [depth= 3] . ( 1182 sec) [ -292686.1036] [79191] [depth= 6] . ( 1188 sec) [ -292640.3843] [79183] [depth= 2] . ( 1200 sec) [ -292639.8252] [79188] [depth= 2] . ( 1208 sec) [ -292625.6603] [79191] [depth= 2] . ( 1213 sec) [ -292604.4418] [79182] [depth= 4] . ( 1218 sec) [ -292452.5991] [79145] [depth= 13] . ( 1224 sec) [ -292442.3499] [79149] [depth= 1] . ( 1229 sec) [ -292417.4564] [79139] [depth= 6] . ( 1234 sec) [ -292410.0087] [79134] [depth= 1] . ( 1239 sec) [ -292364.4197] [79134] [depth= 3] . ( 1243 sec) [ -292360.0948] [79134] [depth= 1] . ( 1248 sec) [ -292313.8224] [79119] [depth= 2] . ( 1268 sec) [ -292272.5920] [79123] [depth= 15] . ( 1276 sec) [ -292245.4844] [79108] [depth= 7] . ( 1281 sec) [ -292213.6291] [79056] [depth= 13] . ( 1293 sec) [ -292180.6402] [79041] [depth= 12] . ( 1300 sec) [ -292174.4073] [79042] [depth= 1] . ( 1307 sec) [ -292128.4316] [79037] [depth= 1] . ( 1312 sec) [ -292086.0360] [78987] [depth= 14] . ( 1320 sec) [ -292059.1510] [78987] [depth= 6] . ( 1329 sec) [ -292049.6746] [78988] [depth= 2] . ( 1342 sec) [ -292037.7445] [78989] [depth= 3] . ( 1347 sec) [ -292036.8985] [78990] [depth= 3] . ( 1353 sec) [ -292034.1838] [78990] [depth= 1] . ( 1360 sec) [ -292033.6222] [78975] [depth= 3] . ( 1372 sec) [ -292021.4824] [78969] [depth= 13] . ( 1377 sec) [ -291935.9038] [78932] [depth= 8] . ( 1382 sec) [ -291903.2613] [78914] [depth= 1] . ( 1389 sec) [ -291874.8397] [78918] [depth= 1] . ( 1395 sec) [ -291866.0325] [78920] [depth= 1] . ( 1398 sec) [ -291851.7173] [78914] [depth= 1] . ( 1403 sec) [ -291776.9537] [78918] [depth= 1] . ( 1409 sec) [ -291776.0014] [78913] [depth= 1] . ( 1416 sec) [ -291773.3783] [78886] [depth= 7] . ( 1422 sec) [ -291744.0531] [78870] [depth= 14] . ( 1427 sec) [ -291717.5948] [78768] [depth= 20] . ( 1434 sec) [ -291618.0244] [78716] [depth= 7] . ( 1448 sec) [ -291590.3051] [78714] [depth= 2] . ( 1454 sec) [ -291467.5139] [78656] [depth= 12] . ( 1468 sec) [ -291341.4730] [78627] [depth= 13] . ( 1473 sec) [ -291255.0369] [78559] [depth= 12] . ( 1477 sec) [ -291253.6973] [78552] [depth= 1] . ( 1482 sec) [ -291249.1542] [78541] [depth= 3] . ( 1487 sec) [ -291235.4594] [78527] [depth= 1] . ( 1500 sec) [ -291227.3910] [78517] [depth= 1] . ( 1505 sec) [ -290970.0493] [78380] [depth= 20] . ( 1510 sec) [ -290838.0022] [78315] [depth= 13] . ( 1517 sec) [ -290836.3298] [78313] [depth= 2] . ( 1525 sec) [ -290836.1789] [78299] [depth= 1] . ( 1541 sec) [ -290782.7953] [78274] [depth= 7] . ( 1549 sec) [ -290781.1582] [78264] [depth= 1] . ( 1554 sec) [ -290778.3351] [78270] [depth= 1] . ( 1559 sec) [ -290771.7378] [78278] [depth= 1] . ( 1570 sec) [ -290750.1887] [78270] [depth= 2] . ( 1576 sec) [ -290744.7932] [78271] [depth= 2] . ( 1581 sec) [ -290743.2534] [78265] [depth= 1] . ( 1586 sec) [ -290733.5810] [78263] [depth= 1] . ( 1592 sec) [ -290714.0513] [78251] [depth= 6] . ( 1597 sec) [ -290633.5689] [78174] [depth= 10] . ( 1602 sec) [ -290488.6421] [78082] [depth= 11] . ( 1607 sec) [ -290480.9458] [78064] [depth= 6] . ( 1612 sec) [ -290275.3475] [77981] [depth= 18] . ( 1620 sec) [ -290248.5210] [77970] [depth= 6] . ( 1625 sec) [ -290186.6969] [77928] [depth= 6] . ( 1630 sec) [ -290133.5282] [77917] [depth= 1] . ( 1634 sec) [ -290122.1395] [77920] [depth= 2] . ( 1641 sec) [ -290119.8249] [77924] [depth= 1] . ( 1646 sec) [ -290027.1127] [77879] [depth= 9] . ( 1650 sec) [ -290024.4042] [77880] [depth= 2] . ( 1655 sec) [ -290009.4816] [77862] [depth= 2] . ( 1658 sec) [ -289994.5726] [77858] [depth= 1] . ( 1666 sec) [ -289993.4455] [77860] [depth= 2] . ( 1674 sec) [ -289990.6873] [77860] [depth= 5] . ( 1679 sec) [ -289987.8441] [77855] [depth= 2] . ( 1685 sec) [ -289935.9725] [77852] [depth= 1] . ( 1691 sec) [ -289935.2366] [77854] [depth= 1] . ( 1697 sec) [ -289932.3823] [77800] [depth= 5] . ( 1715 sec) [ -289931.4752] [77804] [depth= 5] . ( 1723 sec) [ -289905.3202] [77797] [depth= 3] . ( 1728 sec) [ -289867.7741] [77782] [depth= 1] . ( 1735 sec) [ -289862.7589] [77783] [depth= 5] . ( 1741 sec) [ -289832.7312] [77730] [depth= 11] . ( 1746 sec) [ -289828.7458] [77722] [depth= 2] . ( 1751 sec) [ -289816.9880] [77719] [depth= 2] . ( 1758 sec) [ -289780.8680] [77720] [depth= 2] . ( 1769 sec) [ -289762.6045] [77711] [depth= 1] . ( 1777 sec) [ -289757.5409] [77711] [depth= 1] . ( 1782 sec) [ -289733.0954] [77703] [depth= 4] . ( 1788 sec) [ -289726.4407] [77706] [depth= 2] . ( 1793 sec) [ -289710.6140] [77709] [depth= 1] . ( 1798 sec) [ -289661.0178] [77718] [depth= 1] . ( 1804 sec) [ -289651.7835] [77714] [depth= 2] . ( 1813 sec) [ -289643.2981] [77707] [depth= 2] . ( 1819 sec) [ -289640.4432] [77703] [depth= 3] . ( 1824 sec) [ -289431.4284] [77617] [depth= 15] . ( 1829 sec) [ -289368.7208] [77600] [depth= 8] . ( 1835 sec) [ -289357.9146] [77589] [depth= 6] . ( 1840 sec) [ -289357.1643] [77578] [depth= 6] . ( 1847 sec) [ -289318.7070] [77568] [depth= 1] . ( 1851 sec) [ -289304.5238] [77569] [depth= 1] . ( 1855 sec) [ -289276.3329] [77553] [depth= 1] . ( 1863 sec) [ -289275.9685] [77541] [depth= 1] . ( 1873 sec) [ -289274.8881] [77545] [depth= 1] . ( 1890 sec) [ -289255.2460] [77522] [depth= 2] . ( 1896 sec) [ -289250.3429] [77526] [depth= 1] . ( 1901 sec) [ -289248.7209] [77530] [depth= 1] . ( 1908 sec) [ -289240.3271] [77531] [depth= 1] . ( 1912 sec) [ -289227.0652] [77529] [depth= 1] . ( 1917 sec) [ -289222.8074] [77515] [depth= 2] . ( 1922 sec) [ -289211.9071] [77510] [depth= 3] . ( 1927 sec) [ -289207.9211] [77502] [depth= 1] . ( 1932 sec) [ -289179.7878] [77505] [depth= 1] . ( 1940 sec) [ -289171.2341] [77501] [depth= 1] . ( 1946 sec) [ -289168.6773] [77506] [depth= 1] . ( 1963 sec) [ -289132.0680] [77491] [depth= 3] . ( 1969 sec) [ -289127.9904] [77487] [depth= 1] . ( 1976 sec) [ -288924.5287] [77443] [depth= 2] . ( 1980 sec) [ -288923.0688] [77442] [depth= 1] . ( 1993 sec) [ -288919.3139] [77443] [depth= 2] . ( 2002 sec) [ -288902.8924] [77437] [depth= 8] . ( 2010 sec) [ -288902.0767] [77436] [depth= 1] . ( 2015 sec) [ -288800.4032] [77419] [depth= 8] . ( 2020 sec) [ -288706.6482] [77387] [depth= 8] . ( 2025 sec) [ -288705.2945] [77385] [depth= 1] . ( 2033 sec) [ -288694.9000] [77386] [depth= 1] . ( 2038 sec) [ -288685.4343] [77391] [depth= 1] . ( 2043 sec) [ -288603.5902] [77393] [depth= 3] . ( 2049 sec) [ -288600.1639] [77396] [depth= 1] . ( 2055 sec) [ -288598.6234] [77391] [depth= 1] . ( 2060 sec) [ -288583.1983] [77396] [depth= 1] . ( 2069 sec) [ -288578.6000] [77397] [depth= 2] . ( 2079 sec) [ -288552.3678] [77389] [depth= 1] . ( 2084 sec) [ -288549.1807] [77386] [depth= 1] . ( 2092 sec) [ -288529.3079] [77372] [depth= 4] . ( 2099 sec) [ -288517.4489] [77366] [depth= 1] . ( 2109 sec) [ -288511.7595] [77359] [depth= 1] . ( 2120 sec) [ -288500.3468] [77364] [depth= 1] . ( 2132 sec) [ -288492.3587] [77364] [depth= 1] . ( 2137 sec) [ -288482.8762] [77348] [depth= 6] . ( 2143 sec) [ -288356.0716] [77346] [depth= 1] . ( 2148 sec) [ -288346.2733] [77344] [depth= 3] . ( 2153 sec) [ -288328.8106] [77339] [depth= 2] . ( 2158 sec) [ -288183.2084] [77250] [depth= 15] . ( 2171 sec) [ -288180.0511] [77254] [depth= 1] . ( 2177 sec) [ -288178.4553] [77241] [depth= 6] . ( 2182 sec) [ -288134.1622] [77229] [depth= 1] . ( 2187 sec) [ -288120.9002] [77223] [depth= 3] . ( 2201 sec) [ -288088.1777] [77204] [depth= 2] . ( 2211 sec) [ -288088.1382] [77201] [depth= 2] . ( 2224 sec) [ -288050.0643] [77201] [depth= 1] . ( 2229 sec) [ -287994.1623] [77184] [depth= 6] . ( 2234 sec) [ -287985.1085] [77187] [depth= 1] . ( 2239 sec) [ -287983.7215] [77179] [depth= 1] . ( 2247 sec) [ -287954.7491] [77174] [depth= 5] . ( 2252 sec) [ -287941.0277] [77205] [depth= 4] . ( 2257 sec) [ -287915.3622] [77199] [depth= 2] . ( 2263 sec) [ -287904.5560] [77202] [depth= 1] . ( 2268 sec) [ -287898.5251] [77198] [depth= 1] . ( 2275 sec) [ -287886.1992] [77168] [depth= 4] . ( 2279 sec) [ -287876.2141] [77166] [depth= 1] . ( 2284 sec) [ -287857.7507] [77169] [depth= 1] . ( 2291 sec) [ -287849.1360] [77168] [depth= 1] . ( 2297 sec) [ -287827.1198] [77172] [depth= 1] . ( 2302 sec) [ -287794.8558] [77161] [depth= 3] . ( 2307 sec) [ -287740.3668] [77118] [depth= 9] . ( 2313 sec) [ -287706.8132] [77111] [depth= 2] . ( 2317 sec) [ -287673.5854] [77104] [depth= 2] . ( 2322 sec) [ -287657.6653] [77096] [depth= 1] . ( 2327 sec) [ -287643.0492] [77092] [depth= 1] . ( 2336 sec) [ -287617.7652] [77082] [depth= 5] . ( 2341 sec) [ -287612.7558] [77086] [depth= 1] . ( 2346 sec) [ -287591.6879] [77079] [depth= 1] . ( 2355 sec) [ -287588.2531] [77085] [depth= 1] . ( 2362 sec) [ -287562.3657] [77090] [depth= 1] . ( 2370 sec) [ -287527.0738] [77082] [depth= 6] . ( 2377 sec) [ -287526.4430] [77086] [depth= 3] . ( 2380 sec) [ -287508.1925] [77086] [depth= 1] . ( 2386 sec) [ -287499.5119] [77071] [depth= 2] . ( 2391 sec) [ -287490.8664] [77073] [depth= 1] . ( 2397 sec) [ -287490.1702] [77073] [depth= 1] . ( 2400 sec) [ -287466.0150] [77074] [depth= 1] . ( 2405 sec) [ -287460.8149] [77072] [depth= 1] . ( 2417 sec) [ -287347.5940] [77020] [depth= 5] . ( 2427 sec) [ -287346.3913] [77025] [depth= 1] . ( 2435 sec) [ -287335.5019] [77027] [depth= 1] . ( 2441 sec) [ -287175.9145] [76991] [depth= 1] . ( 2448 sec) [ -287166.9049] [76983] [depth= 6] . ( 2454 sec) [ -287164.5053] [76982] [depth= 2] . ( 2462 sec) [ -287164.0981] [76980] [depth= 1] . ( 2465 sec) [ -287158.3805] [76975] [depth= 1] . ( 2470 sec) [ -287157.2735] [76972] [depth= 1] . ( 2475 sec) [ -287155.8802] [76977] [depth= 1] . ( 2482 sec) [ -287155.0278] [76979] [depth= 1] . ( 2486 sec) [ -287122.5810] [76965] [depth= 2] . ( 2493 sec) [ -287105.3047] [76961] [depth= 1] . ( 2503 sec) [ -287089.4450] [76965] [depth= 1] . ( 2509 sec) [ -287086.2761] [76968] [depth= 4] . ( 2517 sec) [ -287085.2523] [76973] [depth= 2] . ( 2525 sec) [ -287067.5861] [76969] [depth= 2] . ( 2530 sec) [ -287062.9118] [76967] [depth= 5] . ( 2536 sec) [ -287047.9515] [76968] [depth= 2] . ( 2541 sec) [ -287047.8600] [76968] [depth= 1] . ( 2548 sec) [ -287044.7627] [76970] [depth= 1] . ( 2554 sec) [ -287004.3306] [76964] [depth= 1] . ( 2557 sec) [ -286999.6479] [76961] [depth= 2] . ( 2563 sec) [ -286998.1916] [76963] [depth= 1] . ( 2568 sec) [ -286960.6007] [76963] [depth= 15] . ( 2574 sec) [ -286917.0637] [76960] [depth= 3] . ( 2579 sec) [ -286902.5756] [76955] [depth= 1] . ( 2584 sec) [ -286902.1719] [76958] [depth= 1] . ( 2590 sec) [ -286896.4176] [76959] [depth= 3] . ( 2600 sec) [ -286893.0161] [76954] [depth= 1] . ( 2608 sec) [ -286880.5405] [76985] [depth= 1] . ( 2611 sec) [ -286868.4257] [76980] [depth= 1] . ( 2618 sec) [ -286865.2094] [76981] [depth= 2] . ( 2626 sec) [ -286862.6046] [76980] [depth= 1] . ( 2630 sec) [ -286846.6628] [76979] [depth= 1] . ( 2635 sec) [ -286831.0829] [76972] [depth= 2] . ( 2640 sec) [ -286819.3872] [76956] [depth= 2] . ( 2647 sec) [ -286815.1313] [76954] [depth= 2] . ( 2654 sec) [ -286799.9326] [76927] [depth= 2] . ( 2664 sec) [ -286793.3064] [76919] [depth= 1] . ( 2667 sec) [ -286780.6031] [76922] [depth= 1] . ( 2673 sec) [ -286756.2047] [76915] [depth= 1] . ( 2678 sec) [ -286749.3812] [76914] [depth= 1] . ( 2684 sec) [ -286721.5400] [76911] [depth= 1] . ( 2688 sec) [ -286717.0198] [76919] [depth= 2] . ( 2694 sec) [ -286705.8113] [76914] [depth= 2] . ( 2727 sec) [ -284508.3981] [Branch lengths ] . ( 2849 sec) [ -284375.9968] [GTR parameters ] . ( 2858 sec) [ -284217.0985] [Alpha ][ 0.900758] . ( 2889 sec) [ -284216.4909] [76911] [depth= 1] . ( 2910 sec) [ -284212.8858] [76913] [depth= 1] . ( 2922 sec) [ -284196.1680] [76911] [depth= 3] . ( 2966 sec) [ -284190.0277] [76907] [depth= 1] . ( 2974 sec) [ -284177.7807] [76892] [depth= 1] . ( 2990 sec) [ -284176.9451] [76900] [depth= 5] . ( 3004 sec) [ -284153.0886] [76893] [depth= 6] . ( 3010 sec) [ -284142.4593] [76886] [depth= 3] . ( 3021 sec) [ -284000.3303] [76830] [depth= 8] . ( 3040 sec) [ -283986.8286] [76823] [depth= 3] . ( 3062 sec) [ -283986.4005] [76817] [depth= 1] . ( 3078 sec) [ -283972.0955] [76816] [depth= 2] . ( 3093 sec) [ -283971.3743] [76812] [depth= 2] . ( 3114 sec) [ -283966.5007] [76805] [depth= 5] . ( 3126 sec) [ -283955.6062] [76793] [depth= 1] . ( 3138 sec) [ -283955.1168] [76791] [depth= 1] . ( 3144 sec) [ -283938.7446] [76786] [depth= 1] . ( 3164 sec) [ -283902.7152] [76765] [depth= 7] . ( 3170 sec) [ -283898.8513] [76770] [depth= 1] . ( 3173 sec) [ -283892.0490] [76768] [depth= 1] . ( 3190 sec) [ -283891.4219] [76766] [depth= 1] . ( 3224 sec) [ -283795.1098] [76710] [depth= 14] . ( 3232 sec) [ -283789.9090] [76709] [depth= 2] . ( 3253 sec) [ -283780.3966] [76722] [depth= 1] . ( 3259 sec) [ -283773.9532] [76721] [depth= 2] . ( 3262 sec) [ -283769.4025] [76723] [depth= 1] . ( 3270 sec) [ -283768.0138] [76727] [depth= 1] . ( 3280 sec) [ -283764.1345] [76728] [depth= 1] . ( 3296 sec) [ -283760.1683] [76733] [depth= 1] . ( 3301 sec) [ -283758.8024] [76733] [depth= 1] . ( 3309 sec) [ -283757.4927] [76734] [depth= 1] . ( 3333 sec) [ -283740.8891] [76726] [depth= 3] . ( 3348 sec) [ -283739.8057] [76727] [depth= 1] . ( 3365 sec) [ -283736.3850] [76728] [depth= 1] . ( 3387 sec) [ -283705.7057] [76705] [depth= 12] . ( 3393 sec) [ -283702.9192] [76709] [depth= 1] . ( 3398 sec) [ -283664.6227] [76698] [depth= 12] . ( 3434 sec) [ -283659.8948] [76699] [depth= 1] . ( 3442 sec) [ -283650.9247] [76699] [depth= 3] . ( 3447 sec) [ -283644.7007] [76694] [depth= 1] . ( 3462 sec) [ -283639.9686] [76688] [depth= 1] . ( 3481 sec) [ -283628.4822] [76689] [depth= 1] . ( 3507 sec) [ -283627.7036] [76690] [depth= 1] . ( 3517 sec) [ -283532.7748] [76641] [depth= 16] . ( 3520 sec) [ -283519.2721] [76627] [depth= 1] . ( 3546 sec) [ -283518.9791] [76623] [depth= 1] . ( 3557 sec) [ -283517.8069] [76624] [depth= 4] . ( 3574 sec) [ -283513.2240] [76623] [depth= 1] . ( 3584 sec) [ -283513.1584] [76627] [depth= 1] . ( 3614 sec) [ -283497.9484] [76624] [depth= 4] . ( 3637 sec) [ -283492.3716] [76619] [depth= 1] . ( 3640 sec) [ -283480.8494] [76624] [depth= 1] . ( 3648 sec) [ -283475.7612] [76629] [depth= 1] . ( 3686 sec) [ -283466.0098] [76619] [depth= 3] . ( 3693 sec) [ -283463.8580] [76614] [depth= 1] . ( 3701 sec) [ -283460.2002] [76618] [depth= 1] . ( 3718 sec) [ -283452.9930] [76620] [depth= 1] . ( 3723 sec) [ -283451.1568] [76621] [depth= 1] . ( 3750 sec) [ -283447.8154] [76612] [depth= 3] . ( 3768 sec) [ -283445.1564] [76612] [depth= 1] . ( 3780 sec) [ -283442.6611] [76609] [depth= 1] . ( 3795 sec) [ -283441.6162] [76606] [depth= 2] . ( 3839 sec) [ -283433.2778] [76599] [depth= 1] . ( 3847 sec) [ -283413.9560] [76594] [depth= 1] . ( 3861 sec) [ -283413.5532] [76589] [depth= 1] . ( 3886 sec) [ -283408.8971] [76594] [depth= 1] . ( 3891 sec) [ -283405.7146] [76589] [depth= 1] . ( 3897 sec) [ -283403.0479] [76592] [depth= 1] . ( 3903 sec) [ -283399.8178] [76601] [depth= 1] . ( 3915 sec) [ -283316.7646] [76574] [depth= 11] . ( 3934 sec) [ -283311.7454] [76570] [depth= 1] . ( 3939 sec) [ -283302.6567] [76571] [depth= 1] . ( 3954 sec) [ -283290.7903] [76571] [depth= 3] . ( 3972 sec) [ -283284.9172] [76566] [depth= 1] . ( 3984 sec) [ -283271.2763] [76559] [depth= 3] . ( 3989 sec) [ -283268.3275] [76560] [depth= 2] . ( 4004 sec) [ -283267.7885] [76557] [depth= 1] . ( 4012 sec) [ -283265.0155] [76555] [depth= 1] . ( 4027 sec) [ -283262.8646] [76549] [depth= 1] . ( 4032 sec) [ -283243.8246] [76539] [depth= 1] . ( 4041 sec) [ -283239.3768] [76544] [depth= 1] . ( 4054 sec) [ -283236.8633] [76545] [depth= 1] . ( 4062 sec) [ -283234.7334] [76543] [depth= 1] . ( 4075 sec) [ -283233.6375] [76548] [depth= 1] . ( 4082 sec) [ -283229.4541] [76544] [depth= 3] . ( 4088 sec) [ -283227.3102] [76544] [depth= 1] . ( 4102 sec) [ -283226.2479] [76544] [depth= 1] . ( 4108 sec) [ -283190.9143] [76517] [depth= 5] . ( 4113 sec) [ -283187.0390] [76497] [depth= 10] . ( 4118 sec) [ -283182.9771] [76496] [depth= 1] . ( 4135 sec) [ -283176.2095] [76500] [depth= 1] . ( 4148 sec) [ -283174.7328] [76503] [depth= 2] . ( 4182 sec) [ -283173.6559] [76508] [depth= 3] . ( 4187 sec) [ -283167.3516] [76508] [depth= 1] . ( 4190 sec) [ -283166.3185] [76510] [depth= 1] . ( 4195 sec) [ -283155.1229] [76482] [depth= 3] . ( 4201 sec) [ -283150.0666] [76472] [depth= 1] . ( 4223 sec) [ -283149.7547] [76472] [depth= 1] . ( 4247 sec) [ -283138.0674] [76473] [depth= 1] . ( 4256 sec) [ -283131.7725] [76466] [depth= 10] . ( 4261 sec) [ -283128.5950] [76454] [depth= 1] . ( 4307 sec) [ -283121.0662] [76446] [depth= 1] . ( 4322 sec) [ -283118.0076] [76446] [depth= 1] . ( 4345 sec) [ -283116.9547] [76440] [depth= 1] . ( 4356 sec) [ -283100.6246] [76433] [depth= 3] . ( 4363 sec) [ -283097.1313] [76424] [depth= 2] . ( 4371 sec) [ -283084.6651] [76423] [depth= 1] . ( 4382 sec) [ -283084.1413] [76427] [depth= 2] . ( 4387 sec) [ -283083.8160] [76431] [depth= 1] . ( 4399 sec) [ -283083.4037] [76423] [depth= 1] . ( 4418 sec) [ -283081.7792] [76436] [depth= 1] . ( 4442 sec) [ -283080.5811] [76434] [depth= 1] . ( 4481 sec) [ -283079.6102] [76434] [depth= 1] . ( 4528 sec) [ -283077.3569] [76436] [depth= 1] . ( 4540 sec) [ -283075.8758] [76435] [depth= 1] . ( 4559 sec) [ -283074.7650] [76429] [depth= 1] . ( 4568 sec) [ -283074.6471] [76427] [depth= 1] . ( 4575 sec) [ -283070.9272] [76432] [depth= 1] . ( 4597 sec) [ -283069.4807] [76435] [depth= 1] . ( 4630 sec) [ -283068.3214] [76436] [depth= 1] . ( 4641 sec) [ -283066.7372] [76435] [depth= 1] . ( 4745 sec) [ -282516.1836] [Branch lengths ] . ( 4792 sec) [ -282515.6887] [GTR parameters ] . ( 4801 sec) [ -282515.6251] [Alpha ][ 0.904799] . ( 4911 sec) [ -282509.5894] [76432] [depth= 1] . ( 5001 sec) [ -282509.0105] [76428] [depth= 1] . ( 5041 sec) [ -282507.0548] [76427] [depth= 1] . ( 5280 sec) [ -282440.2969] [76448] [depth= 32] . ( 5396 sec) [ -282418.1717] [76451] [depth= 12] . ( 5401 sec) [ -282417.4795] [76453] [depth= 1] . ( 5543 sec) [ -282414.9972] [76445] [depth= 1] . ( 5601 sec) [ -282402.4194] [76435] [depth= 3] . ( 5612 sec) [ -282402.0612] [76437] [depth= 2] . ( 5651 sec) [ -282401.6248] [76436] [depth= 3] . ( 5734 sec) [ -282397.6981] [76438] [depth= 2] . ( 5776 sec) [ -282379.6253] [76427] [depth= 3] . ( 5789 sec) [ -282379.4963] [76430] [depth= 1] . ( 5823 sec) [ -282379.4110] [76425] [depth= 1] . ( 5844 sec) [ -282377.7085] [76429] [depth= 1] . ( 5849 sec) [ -282375.3101] [76430] [depth= 1] . ( 5855 sec) [ -282373.5302] [76432] [depth= 2] . ( 5881 sec) [ -282373.4443] [76436] [depth= 2] . ( 5905 sec) [ -282372.1643] [76438] [depth= 1] . ( 5954 sec) [ -282371.9529] [76437] [depth= 1] . ( 6084 sec) [ -282370.2621] [76439] [depth= 2] . ( 6256 sec) [ -282369.7227] [76438] [depth= 1] . ( 6337 sec) [ -282368.9031] [76437] [depth= 1] . ( 6425 sec) [ -282242.2679] [Branch lengths ] . ( 6472 sec) [ -282241.7740] [GTR parameters ] . ( 6482 sec) [ -282241.7310] [Alpha ][ 0.901439] . ( 6818 sec) [ -282239.7389] [76437] [depth= 1] . ( 8059 sec) [ -282217.4316] [Branch lengths ] . ( 8146 sec) [ -282217.3501] [GTR parameters ] . ( 8155 sec) [ -282217.3314] [Alpha ][ 0.899223] . ( 9732 sec) [ -282213.8931] [Branch lengths ] . (10031 sec) [ -282213.8515] [76435] [depth= 2] . (11633 sec) [ -282211.9398] [76428] [depth= 1] . (12587 sec) [ -282211.7158] [76427] [depth= 1] . (12607 sec) [ -282211.2092] [76451] [depth= 5] . (12882 sec) [ -282175.2144] [76460] [depth= 4] . (13008 sec) [ -282172.9908] [76464] [depth= 1] . (13195 sec) [ -282171.8463] [76471] [depth= 1] . (13203 sec) [ -282168.8781] [76481] [depth= 1] . (13953 sec) [ -282168.1771] [76488] [depth= 1] . (14802 sec) [ -282167.9517] [76500] [depth= 1] . (14996 sec) [ -282158.0727] [Branch lengths ] . (15075 sec) [ -282158.0335] [GTR parameters ] . (15084 sec) [ -282157.9108] [Alpha ][ 0.893731] . (15643 sec) [ -282152.9648] [76496] [depth= 1] . (16169 sec) [ -282152.5744] [76498] [depth= 1] . (16300 sec) [ -282152.4164] [76491] [depth= 2] . (17475 sec) [ -282152.3562] [76499] [depth= 1] . (17645 sec) [ -282152.3060] [76496] [depth= 1] . (18236 sec) [ -282150.5440] [76483] [depth= 1] . (20337 sec) [ -282144.9591] [Branch lengths ] . (20426 sec) [ -282144.9513] [GTR parameters ] . (20434 sec) [ -282144.9503] [Alpha ][ 0.892837] . (22735 sec) [ -282144.8218] [76493] [depth= 1] . (25658 sec) [ -282142.5424] [Branch lengths ] . (25679 sec) [ -282142.5422] [GTR parameters ] . (25687 sec) [ -282142.5422] [Alpha ][ 0.892837] . (25981 sec) [ -282142.4691] [76501] [depth= 1] . (30912 sec) [ -282136.2647] [Branch lengths ] . (30933 sec) [ -282136.2632] [GTR parameters ] . (30941 sec) [ -282136.2632] [Alpha ][ 0.892837] . (36161 sec) [ -282130.4995] [Branch lengths ] . (36164 sec) [ -282130.4995] [Topology ] . (36243 sec) [ -282127.9995] [Topology ] . (36322 sec) [ -282126.1521] [Topology ] . (36401 sec) [ -282125.7687] [Topology ] . (36479 sec) [ -282125.6323] [Topology ] . (36558 sec) [ -282125.5777] [Topology ] . (36637 sec) [ -282125.5562] [Topology ] . (36715 sec) [ -282125.5504] [Topology ] . (36737 sec) [ -282125.5460] [GTR parameters ] . (36745 sec) [ -282125.5460] [Alpha ][ 0.892837] . (36748 sec) [ -282125.5460] [Topology ] . (36826 sec) [ -282125.5482] [Topology ] . Moving backward . (36833 sec) [ -282125.4975] [Topology ] . (36912 sec) [ -282125.4939] [Topology ] . (36991 sec) [ -282125.4922] [Topology ] . (37069 sec) [ -282125.4915] [Topology ] . (37091 sec) [ -282125.4913] [GTR parameters ] . (37099 sec) [ -282125.4913] [Alpha ][ 0.892837] . (37102 sec) [ -282125.4913] [Topology ] . (37180 sec) [ -282125.4910] [Topology ] . (37202 sec) [ -282125.4910] [GTR parameters ] . (37210 sec) [ -282125.4910] [Alpha ][ 0.892837] . Checking for NNIs, optimizing five branches... . (38005 sec) [ -282124.6198] [Topology ] . Checking for NNIs, optimizing five branches... . (38802 sec) [ -282124.3849] [Topology ] . Checking for NNIs, optimizing five branches... . (39601 sec) [ -282124.3428] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -282124.342849. . Printing the most likely tree in file 'nucleic_M4055_306x7062_2008.phy_phyml_tree.txt'... . Time used 11h13m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 40429.61user 0.00system 11:14:03elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps