.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2623_139x1044_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 : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 959 patterns found. (out of a total of 1044 sites) . 202 sites without polymorphism (19.35%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 71Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 13 sec) [ -48412.0933] [GTR parameters ] . ( 14 sec) [ -47896.6604] [Alpha ][ 0.500960] . ( 14 sec) [ -47896.6604] [Topology ] . ( 19 sec) [ -46842.0254] [Topology ] . ( 25 sec) [ -46574.5707] [Topology ] . ( 31 sec) [ -46466.2556] [Topology ] . ( 37 sec) [ -46392.6354] [Topology ] . ( 42 sec) [ -46362.0933] [Topology ] . ( 47 sec) [ -46342.1045] [Topology ] . ( 53 sec) [ -46333.8995] [Topology ] . ( 59 sec) [ -46304.5516] [Topology ] . ( 64 sec) [ -46279.5135] [Topology ] . ( 79 sec) [ -46184.8533] [GTR parameters ] . ( 80 sec) [ -46184.4821] [Alpha ][ 0.511611] . ( 80 sec) [ -46184.4821] [Topology ] . ( 85 sec) [ -46167.1499] [Topology ] . ( 91 sec) [ -46151.3147] [Topology ] . ( 96 sec) [ -46138.3074] [Topology ] . ( 102 sec) [ -46135.8864] [Topology ] . ( 108 sec) [ -46120.4211] [Topology ] . ( 113 sec) [ -46110.9562] [Topology ] . ( 119 sec) [ -46106.1377] [Topology ] . ( 124 sec) [ -46091.5607] [Topology ] . ( 130 sec) [ -46085.7800] [Topology ] . ( 143 sec) [ -46071.4695] [GTR parameters ] . ( 144 sec) [ -46071.0192] [Alpha ][ 0.522934] . ( 144 sec) [ -46071.0192] [Topology ] . ( 150 sec) [ -46059.5651] [Topology ] . ( 155 sec) [ -46049.7743] [Topology ] . ( 161 sec) [ -46047.5282] [Topology ] . ( 166 sec) [ -46045.6369] [Topology ] . ( 172 sec) [ -46045.0146] [Topology ] . ( 177 sec) [ -46044.6647] [Topology ] . ( 183 sec) [ -46044.4817] [Topology ] . ( 189 sec) [ -46044.4043] [Topology ] . ( 194 sec) [ -46044.3553] [Topology ] . Checking for NNIs, optimizing five branches... . ( 257 sec) [ -46042.9471] [Topology ] . ( 262 sec) [ -46042.8071] [GTR parameters ] . ( 262 sec) [ -46042.8071] [Alpha ][ 0.522934] . ( 263 sec) [ -46042.8071] [Topology ] . ( 268 sec) [ -46042.7034] [Topology ] . ( 274 sec) [ -46042.6692] [Topology ] . ( 279 sec) [ -46042.6479] [Topology ] . ( 285 sec) [ -46042.6315] [Topology ] . ( 291 sec) [ -46042.6181] [Topology ] . ( 296 sec) [ -46042.6066] [Topology ] . Checking for NNIs, optimizing five branches... . ( 353 sec) [ -46041.5640] [Topology ] . ( 358 sec) [ -46041.5547] [GTR parameters ] . ( 358 sec) [ -46041.5547] [Alpha ][ 0.522934] . ( 358 sec) [ -46041.5547] [Topology ] . ( 364 sec) [ -46041.3916] [Topology ] . ( 370 sec) [ -46041.3637] [Topology ] . ( 375 sec) [ -46041.3520] [Topology ] . ( 381 sec) [ -46041.3438] [Topology ] . ( 386 sec) [ -46041.3421] [Topology ] . ( 392 sec) [ -46039.7492] [Topology ] . ( 397 sec) [ -46037.2589] [Topology ] . ( 403 sec) [ -46035.7809] [Topology ] . ( 409 sec) [ -46035.4547] [Topology ] . Checking for NNIs, optimizing five branches... . ( 470 sec) [ -46032.5470] [Topology ] . ( 476 sec) [ -46032.5264] [GTR parameters ] . ( 476 sec) [ -46032.5248] [Alpha ][ 0.523649] . ( 476 sec) [ -46032.5248] [Topology ] . ( 482 sec) [ -46032.3831] [Topology ] . ( 487 sec) [ -46032.3489] [Topology ] . ( 493 sec) [ -46032.3367] [Topology ] . ( 498 sec) [ -46032.3308] [Topology ] . ( 504 sec) [ -46032.3270] [Topology ] . ( 510 sec) [ -46032.3240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 567 sec) [ -46027.1343] [Topology ] . ( 572 sec) [ -46027.1327] [GTR parameters ] . ( 572 sec) [ -46027.1327] [Alpha ][ 0.523649] . ( 572 sec) [ -46027.1327] [Topology ] . ( 578 sec) [ -46027.0998] [Topology ] . ( 583 sec) [ -46026.0971] [Topology ] . ( 589 sec) [ -46025.9513] [Topology ] . ( 595 sec) [ -46024.7626] [Topology ] . ( 600 sec) [ -46024.4995] [Topology ] . ( 606 sec) [ -46024.2885] [Topology ] . ( 611 sec) [ -46024.1962] [Topology ] . ( 617 sec) [ -46024.1417] [Topology ] . ( 623 sec) [ -46024.1067] [Topology ] . Checking for NNIs, optimizing five branches... . ( 684 sec) [ -46023.6154] [Topology ] . ( 690 sec) [ -46023.5871] [GTR parameters ] . ( 690 sec) [ -46023.5856] [Alpha ][ 0.523125] . ( 690 sec) [ -46023.5856] [Topology ] . ( 696 sec) [ -46016.3974] [Topology ] . ( 702 sec) [ -46015.1162] [Topology ] . ( 707 sec) [ -46014.8537] [Topology ] . ( 713 sec) [ -46014.7646] [Topology ] . ( 718 sec) [ -46014.7284] [Topology ] . ( 724 sec) [ -46014.7106] [Topology ] . ( 730 sec) [ -46014.7000] [Topology ] . Checking for NNIs, optimizing five branches... . ( 787 sec) [ -46009.7342] [Topology ] . ( 792 sec) [ -46009.7240] [GTR parameters ] . ( 793 sec) [ -46009.7215] [Alpha ][ 0.523919] . ( 793 sec) [ -46009.7215] [Topology ] . ( 798 sec) [ -46009.4455] [Topology ] . ( 804 sec) [ -46008.8597] [Topology ] . ( 809 sec) [ -46008.5137] [Topology ] . ( 815 sec) [ -46007.3799] [Topology ] . ( 821 sec) [ -46007.1656] [Topology ] . ( 826 sec) [ -46007.0637] [Topology ] . ( 832 sec) [ -46007.0035] [Topology ] . ( 837 sec) [ -46006.9556] [Topology ] . ( 843 sec) [ -46006.9179] [Topology ] . Checking for NNIs, optimizing five branches... . ( 899 sec) [ -46006.5112] [Topology ] . ( 904 sec) [ -46006.5086] [GTR parameters ] . ( 904 sec) [ -46006.5064] [Alpha ][ 0.524665] . ( 905 sec) [ -46006.5064] [Topology ] . ( 910 sec) [ -46005.6454] [Topology ] . ( 916 sec) [ -46005.2060] [Topology ] . ( 921 sec) [ -46004.9538] [Topology ] . ( 927 sec) [ -46004.7773] [Topology ] . ( 932 sec) [ -46004.6535] [Topology ] . ( 938 sec) [ -46004.5431] [Topology ] . ( 944 sec) [ -46003.9570] [Topology ] . ( 949 sec) [ -46002.9752] [Topology ] . ( 955 sec) [ -46002.9684] [Topology ] . ( 965 sec) [ -46003.4267] [GTR parameters ] . ( 966 sec) [ -46003.4267] [Alpha ][ 0.524665] . ( 966 sec) [ -46003.4267] [Topology ] . ( 971 sec) [ -46003.3818] [Topology ] . ( 977 sec) [ -46004.0080] [Topology ] . Moving backward . ( 977 sec) [ -46002.2125] [Topology ] . ( 983 sec) [ -46002.0682] [Topology ] . ( 988 sec) [ -46002.1911] [Topology ] . Moving backward . ( 989 sec) [ -46001.7457] [Topology ] . ( 994 sec) [ -46001.5749] [Topology ] . ( 1000 sec) [ -46001.5162] [Topology ] . ( 1006 sec) [ -46001.4795] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1067 sec) [ -45999.3953] [Topology ] . ( 1072 sec) [ -45999.3861] [GTR parameters ] . ( 1073 sec) [ -45999.3861] [Alpha ][ 0.524665] . ( 1073 sec) [ -45999.3861] [Topology ] . ( 1079 sec) [ -45999.3173] [Topology ] . ( 1084 sec) [ -45999.2910] [Topology ] . ( 1090 sec) [ -45999.2735] [Topology ] . ( 1095 sec) [ -45999.2597] [Topology ] . ( 1101 sec) [ -45999.2479] [Topology ] . ( 1106 sec) [ -45999.2374] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1161 sec) [ -45999.1785] [Topology ] . ( 1164 sec) [ -45999.1776] [GTR parameters ] . ( 1165 sec) [ -45999.1776] [Alpha ][ 0.524665] . ( 1165 sec) [ -45999.1776] [Topology ] . ( 1170 sec) [ -45999.0388] [Topology ] . ( 1176 sec) [ -45998.9517] [Topology ] . ( 1182 sec) [ -45998.9217] [Topology ] . ( 1187 sec) [ -45998.9030] [Topology ] . ( 1193 sec) [ -45998.8894] [Topology ] . ( 1199 sec) [ -45998.8784] [Topology ] . ( 1204 sec) [ -45998.8691] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1259 sec) [ -45998.8086] [Topology ] . ( 1266 sec) [ -45998.8068] [GTR parameters ] . ( 1267 sec) [ -45998.8068] [Alpha ][ 0.524665] . ( 1267 sec) [ -45998.8068] [Topology ] . ( 1272 sec) [ -45998.8028] [Topology ] . ( 1278 sec) [ -45998.8008] [Topology ] . ( 1284 sec) [ -45998.7997] [Topology ] . ( 1289 sec) [ -45998.7991] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1344 sec) [ -45998.3504] [Topology ] . ( 1348 sec) [ -45998.3498] [GTR parameters ] . ( 1348 sec) [ -45998.3498] [Alpha ][ 0.524665] . ( 1348 sec) [ -45998.3498] [Topology ] . ( 1354 sec) [ -45998.2875] [Topology ] . ( 1360 sec) [ -45998.2766] [Topology ] . ( 1365 sec) [ -45998.2728] [Topology ] . ( 1371 sec) [ -45998.2712] [Topology ] . ( 1376 sec) [ -45998.2705] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1431 sec) [ -45998.2696] [Topology ] . ( 1433 sec) [ -45998.2692] [GTR parameters ] . ( 1434 sec) [ -45998.2692] [Alpha ][ 0.524665] . ( 1434 sec) [ -45998.2692] [Topology ] . ( 1440 sec) [ -45998.2635] [Topology ] . ( 1445 sec) [ -45998.2258] [Topology ] . ( 1451 sec) [ -45998.1315] [Topology ] . ( 1456 sec) [ -45998.0538] [Topology ] . ( 1462 sec) [ -45997.9915] [Topology ] . ( 1468 sec) [ -45997.9382] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1523 sec) [ -45997.6111] [Topology ] . ( 1525 sec) [ -45997.6104] [GTR parameters ] . ( 1526 sec) [ -45997.6083] [Alpha ][ 0.525380] . ( 1526 sec) [ -45997.6083] [Topology ] . ( 1531 sec) [ -45997.5720] [Topology ] . ( 1537 sec) [ -45997.5656] [Topology ] . ( 1542 sec) [ -45997.5635] [Topology ] . ( 1548 sec) [ -45997.5626] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1603 sec) [ -45996.2886] [Topology ] . ( 1604 sec) [ -45996.2857] [GTR parameters ] . ( 1605 sec) [ -45996.2857] [Alpha ][ 0.525380] . ( 1605 sec) [ -45996.2857] [Topology ] . ( 1611 sec) [ -45996.2439] [Topology ] . ( 1616 sec) [ -45996.2361] [Topology ] . ( 1622 sec) [ -45996.2333] [Topology ] . ( 1627 sec) [ -45996.2320] [Topology ] . ( 1633 sec) [ -45996.2314] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1688 sec) [ -45996.2249] [Topology ] . ( 1689 sec) [ -45996.2246] [GTR parameters ] . ( 1690 sec) [ -45996.2246] [Alpha ][ 0.525380] . ( 1690 sec) [ -45996.2246] [Topology ] . ( 1695 sec) [ -45996.2058] [Topology ] . ( 1701 sec) [ -45996.1996] [Topology ] . ( 1706 sec) [ -45996.1962] [Topology ] . ( 1712 sec) [ -45996.1938] [Topology ] . ( 1717 sec) [ -45996.1919] [Topology ] . ( 1723 sec) [ -45996.1904] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1778 sec) [ -45996.1902] [Topology ] . ( 1779 sec) [ -45996.1901] [GTR parameters ] . ( 1779 sec) [ -45996.1901] [Alpha ][ 0.525380] . ( 1780 sec) [ -45996.1901] [Topology ] . ( 1785 sec) [ -45996.1888] [Topology ] . ( 1791 sec) [ -45996.1876] [Topology ] . ( 1796 sec) [ -45996.1867] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1852 sec) [ -45996.1864] [GTR parameters ] . ( 1853 sec) [ -45996.1864] [Alpha ][ 0.525380] . ( 1853 sec) [ -45996.1864] [Topology ] . ( 1858 sec) [ -45996.1855] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1914 sec) [ -45996.1855] [GTR parameters ] . ( 1914 sec) [ -45996.1855] [Alpha ][ 0.525380] . ( 1914 sec) [ -45996.1855] [Topology ] . ( 1920 sec) [ -45996.1849] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 2041 sec) [ -48412.0933] [GTR parameters ] . ( 2042 sec) [ -47896.6604] [Alpha ][ 0.500960] . ( 2043 sec) [ -47896.0418] [11967] [depth= 1] . ( 2043 sec) [ -47889.7491] [11967] [depth= 1] . ( 2043 sec) [ -47889.7184] [11967] [depth= 1] . ( 2045 sec) [ -47884.8015] [11974] [depth= 1] . ( 2045 sec) [ -47884.1065] [11967] [depth= 1] . ( 2045 sec) [ -47880.9605] [11971] [depth= 1] . ( 2047 sec) [ -47880.5369] [11972] [depth= 1] . ( 2048 sec) [ -47774.6680] [11977] [depth= 1] . ( 2048 sec) [ -47746.4842] [11974] [depth= 1] . ( 2050 sec) [ -47691.9593] [11965] [depth= 10] . ( 2050 sec) [ -47678.9464] [11944] [depth= 7] . ( 2051 sec) [ -47669.6854] [11942] [depth= 1] . ( 2051 sec) [ -47665.6354] [11947] [depth= 1] . ( 2051 sec) [ -47658.1171] [11949] [depth= 1] . ( 2052 sec) [ -47653.7020] [11951] [depth= 1] . ( 2053 sec) [ -47638.8318] [11949] [depth= 1] . ( 2054 sec) [ -47590.0596] [11932] [depth= 8] . ( 2054 sec) [ -47526.5165] [11930] [depth= 2] . ( 2055 sec) [ -47522.6803] [11935] [depth= 2] . ( 2055 sec) [ -47520.1468] [11938] [depth= 1] . ( 2056 sec) [ -47509.4594] [11924] [depth= 1] . ( 2057 sec) [ -47504.1025] [11926] [depth= 1] . ( 2057 sec) [ -47503.9077] [11923] [depth= 1] . ( 2058 sec) [ -47435.2032] [11921] [depth= 1] . ( 2058 sec) [ -47434.8112] [11919] [depth= 1] . ( 2059 sec) [ -47434.0884] [11921] [depth= 1] . ( 2060 sec) [ -47408.3802] [11912] [depth= 1] . ( 2060 sec) [ -47406.8051] [11919] [depth= 1] . ( 2061 sec) [ -47398.9314] [11917] [depth= 2] . ( 2061 sec) [ -47395.1014] [11917] [depth= 1] . ( 2062 sec) [ -47393.4723] [11908] [depth= 11] . ( 2062 sec) [ -47322.7419] [11889] [depth= 11] . ( 2062 sec) [ -47322.5987] [11890] [depth= 2] . ( 2063 sec) [ -47317.0897] [11889] [depth= 2] . ( 2063 sec) [ -47306.9571] [11889] [depth= 1] . ( 2063 sec) [ -47296.9314] [11891] [depth= 2] . ( 2065 sec) [ -47293.6942] [11892] [depth= 1] . ( 2065 sec) [ -47292.2287] [11891] [depth= 1] . ( 2065 sec) [ -47291.8039] [11889] [depth= 1] . ( 2066 sec) [ -47291.1975] [11889] [depth= 1] . ( 2066 sec) [ -47268.1630] [11883] [depth= 1] . ( 2066 sec) [ -47260.3346] [11883] [depth= 1] . ( 2067 sec) [ -47233.3725] [11887] [depth= 2] . ( 2067 sec) [ -47220.1232] [11890] [depth= 1] . ( 2068 sec) [ -47215.6834] [11884] [depth= 3] . ( 2068 sec) [ -47129.5826] [11848] [depth= 10] . ( 2069 sec) [ -47121.1510] [11849] [depth= 1] . ( 2069 sec) [ -47119.5980] [11848] [depth= 1] . ( 2069 sec) [ -47112.2688] [11840] [depth= 7] . ( 2070 sec) [ -47107.3666] [11838] [depth= 2] . ( 2070 sec) [ -47086.7604] [11838] [depth= 2] . ( 2070 sec) [ -47060.5077] [11827] [depth= 8] . ( 2072 sec) [ -47058.7698] [11818] [depth= 1] . ( 2072 sec) [ -47057.6055] [11826] [depth= 1] . ( 2072 sec) [ -47040.7615] [11819] [depth= 9] . ( 2073 sec) [ -47040.5780] [11822] [depth= 1] . ( 2075 sec) [ -47039.6206] [11824] [depth= 4] . ( 2075 sec) [ -47039.3092] [11825] [depth= 4] . ( 2075 sec) [ -47034.7995] [11817] [depth= 1] . ( 2076 sec) [ -47029.0497] [11825] [depth= 1] . ( 2077 sec) [ -47025.7197] [11827] [depth= 4] . ( 2078 sec) [ -47012.8470] [11821] [depth= 9] . ( 2078 sec) [ -46954.0708] [11801] [depth= 5] . ( 2079 sec) [ -46930.9528] [11792] [depth= 1] . ( 2079 sec) [ -46929.7693] [11791] [depth= 2] . ( 2080 sec) [ -46929.1534] [11795] [depth= 1] . ( 2080 sec) [ -46927.0353] [11794] [depth= 1] . ( 2081 sec) [ -46923.5160] [11795] [depth= 1] . ( 2082 sec) [ -46918.5777] [11796] [depth= 1] . ( 2082 sec) [ -46916.9645] [11795] [depth= 2] . ( 2082 sec) [ -46911.5131] [11789] [depth= 1] . ( 2083 sec) [ -46903.2673] [11788] [depth= 2] . ( 2083 sec) [ -46900.6212] [11792] [depth= 1] . ( 2084 sec) [ -46898.1654] [11790] [depth= 3] . ( 2085 sec) [ -46897.1996] [11793] [depth= 1] . ( 2085 sec) [ -46893.8600] [11790] [depth= 2] . ( 2086 sec) [ -46893.6068] [11793] [depth= 1] . ( 2087 sec) [ -46886.2323] [11797] [depth= 1] . ( 2088 sec) [ -46880.9043] [11793] [depth= 1] . ( 2088 sec) [ -46878.7707] [11789] [depth= 1] . ( 2089 sec) [ -46876.1304] [11788] [depth= 3] . ( 2089 sec) [ -46873.5800] [11786] [depth= 3] . ( 2089 sec) [ -46873.5416] [11783] [depth= 1] . ( 2090 sec) [ -46868.6886] [11791] [depth= 1] . ( 2090 sec) [ -46856.4919] [11783] [depth= 1] . ( 2090 sec) [ -46854.0401] [11787] [depth= 1] . ( 2091 sec) [ -46851.9353] [11787] [depth= 2] . ( 2091 sec) [ -46849.5299] [11792] [depth= 2] . ( 2092 sec) [ -46835.0678] [11792] [depth= 1] . ( 2092 sec) [ -46834.9489] [11790] [depth= 2] . ( 2092 sec) [ -46834.5417] [11788] [depth= 1] . ( 2093 sec) [ -46821.2412] [11784] [depth= 1] . ( 2093 sec) [ -46817.2874] [11781] [depth= 1] . ( 2093 sec) [ -46815.8002] [11781] [depth= 1] . ( 2094 sec) [ -46809.8727] [11785] [depth= 1] . ( 2094 sec) [ -46809.2413] [11786] [depth= 2] . ( 2095 sec) [ -46807.2359] [11789] [depth= 1] . ( 2095 sec) [ -46799.5849] [11780] [depth= 2] . ( 2097 sec) [ -46791.5239] [11784] [depth= 1] . ( 2098 sec) [ -46785.9409] [11781] [depth= 3] . ( 2098 sec) [ -46783.5217] [11783] [depth= 1] . ( 2098 sec) [ -46783.1387] [11781] [depth= 1] . ( 2100 sec) [ -46779.9018] [11786] [depth= 1] . ( 2100 sec) [ -46777.8240] [11781] [depth= 1] . ( 2101 sec) [ -46770.6025] [11778] [depth= 1] . ( 2101 sec) [ -46756.5826] [11779] [depth= 1] . ( 2101 sec) [ -46748.1042] [11781] [depth= 1] . ( 2102 sec) [ -46718.7961] [11781] [depth= 1] . ( 2102 sec) [ -46702.6952] [11777] [depth= 1] . ( 2103 sec) [ -46686.1965] [11776] [depth= 4] . ( 2103 sec) [ -46685.9180] [11778] [depth= 1] . ( 2103 sec) [ -46683.5880] [11774] [depth= 1] . ( 2104 sec) [ -46681.9225] [11773] [depth= 2] . ( 2104 sec) [ -46672.5150] [11764] [depth= 1] . ( 2105 sec) [ -46669.2363] [11761] [depth= 2] . ( 2105 sec) [ -46666.2447] [11760] [depth= 1] . ( 2106 sec) [ -46665.1375] [11757] [depth= 4] . ( 2106 sec) [ -46660.9781] [11758] [depth= 1] . ( 2107 sec) [ -46640.3396] [11761] [depth= 1] . ( 2107 sec) [ -46622.5552] [11765] [depth= 1] . ( 2108 sec) [ -46621.7140] [11770] [depth= 1] . ( 2108 sec) [ -46616.0759] [11765] [depth= 1] . ( 2108 sec) [ -46598.5865] [11757] [depth= 2] . ( 2109 sec) [ -46593.6260] [11758] [depth= 1] . ( 2109 sec) [ -46591.2225] [11758] [depth= 1] . ( 2110 sec) [ -46588.8665] [11757] [depth= 1] . ( 2110 sec) [ -46574.6584] [11758] [depth= 1] . ( 2111 sec) [ -46571.8866] [11762] [depth= 1] . ( 2111 sec) [ -46569.8995] [11758] [depth= 1] . ( 2113 sec) [ -46569.8870] [11760] [depth= 1] . ( 2114 sec) [ -46568.3421] [11759] [depth= 1] . ( 2114 sec) [ -46567.7925] [11760] [depth= 3] . ( 2115 sec) [ -46566.2911] [11759] [depth= 2] . ( 2115 sec) [ -46565.7276] [11761] [depth= 1] . ( 2116 sec) [ -46562.5362] [11761] [depth= 1] . ( 2116 sec) [ -46561.5999] [11759] [depth= 1] . ( 2116 sec) [ -46559.9442] [11761] [depth= 2] . ( 2117 sec) [ -46555.7153] [11762] [depth= 1] . ( 2118 sec) [ -46550.4855] [11762] [depth= 2] . ( 2118 sec) [ -46550.3427] [11759] [depth= 2] . ( 2118 sec) [ -46549.7750] [11757] [depth= 1] . ( 2119 sec) [ -46547.5104] [11759] [depth= 1] . ( 2119 sec) [ -46547.2786] [11760] [depth= 1] . ( 2121 sec) [ -46286.4111] [Branch lengths ] . ( 2131 sec) [ -46239.2082] [GTR parameters ] . ( 2131 sec) [ -46239.0351] [Alpha ][ 0.492531] . ( 2132 sec) [ -46238.1935] [11760] [depth= 1] . ( 2134 sec) [ -46237.9999] [11765] [depth= 1] . ( 2134 sec) [ -46234.2504] [11767] [depth= 1] . ( 2137 sec) [ -46226.1767] [11761] [depth= 1] . ( 2138 sec) [ -46212.5414] [11746] [depth= 5] . ( 2139 sec) [ -46211.4208] [11738] [depth= 6] . ( 2143 sec) [ -46203.3408] [11739] [depth= 6] . ( 2144 sec) [ -46194.1187] [11735] [depth= 6] . ( 2145 sec) [ -46193.4564] [11731] [depth= 1] . ( 2147 sec) [ -46193.4316] [11731] [depth= 2] . ( 2153 sec) [ -46193.0118] [11728] [depth= 2] . ( 2154 sec) [ -46190.4188] [11718] [depth= 6] . ( 2154 sec) [ -46189.5225] [11716] [depth= 1] . ( 2155 sec) [ -46183.2468] [11710] [depth= 8] . ( 2157 sec) [ -46177.9005] [11706] [depth= 2] . ( 2159 sec) [ -46176.1522] [11705] [depth= 3] . ( 2159 sec) [ -46174.7361] [11707] [depth= 1] . ( 2161 sec) [ -46173.7610] [11707] [depth= 2] . ( 2162 sec) [ -46169.1084] [11698] [depth= 3] . ( 2164 sec) [ -46168.0396] [11702] [depth= 3] . ( 2164 sec) [ -46167.2814] [11702] [depth= 2] . ( 2165 sec) [ -46166.9918] [11700] [depth= 2] . ( 2165 sec) [ -46164.9527] [11700] [depth= 2] . ( 2166 sec) [ -46162.7533] [11703] [depth= 1] . ( 2168 sec) [ -46161.5908] [11702] [depth= 1] . ( 2171 sec) [ -46159.7393] [11704] [depth= 1] . ( 2174 sec) [ -46159.4914] [11705] [depth= 1] . ( 2178 sec) [ -46158.3994] [11707] [depth= 3] . ( 2180 sec) [ -46157.8064] [11711] [depth= 1] . ( 2181 sec) [ -46157.7827] [11709] [depth= 1] . ( 2183 sec) [ -46157.4320] [11713] [depth= 1] . ( 2183 sec) [ -46157.1097] [11712] [depth= 1] . ( 2185 sec) [ -46156.4321] [11710] [depth= 2] . ( 2187 sec) [ -46154.3376] [11713] [depth= 1] . ( 2189 sec) [ -46152.7799] [11713] [depth= 1] . ( 2191 sec) [ -46152.3236] [11718] [depth= 1] . ( 2193 sec) [ -46151.3614] [11721] [depth= 1] . ( 2193 sec) [ -46150.6616] [11718] [depth= 1] . ( 2195 sec) [ -46149.6522] [11721] [depth= 1] . ( 2196 sec) [ -46147.5609] [11716] [depth= 1] . ( 2199 sec) [ -46074.6548] [Branch lengths ] . ( 2207 sec) [ -46071.6534] [GTR parameters ] . ( 2207 sec) [ -46070.1542] [Alpha ][ 0.515258] . ( 2208 sec) [ -46069.8580] [11716] [depth= 1] . ( 2209 sec) [ -46069.5146] [11714] [depth= 1] . ( 2209 sec) [ -46069.4072] [11716] [depth= 1] . ( 2218 sec) [ -46067.8342] [11717] [depth= 6] . ( 2220 sec) [ -46067.3688] [11714] [depth= 1] . ( 2224 sec) [ -46067.3454] [11714] [depth= 2] . ( 2228 sec) [ -46067.0657] [11719] [depth= 1] . ( 2230 sec) [ -46066.7667] [11720] [depth= 1] . ( 2230 sec) [ -46066.6845] [11719] [depth= 1] . ( 2237 sec) [ -46066.5830] [11721] [depth= 1] . ( 2239 sec) [ -46059.0482] [11723] [depth= 6] . ( 2240 sec) [ -46058.9198] [11723] [depth= 1] . ( 2244 sec) [ -46058.8770] [11719] [depth= 1] . ( 2252 sec) [ -46058.3983] [11722] [depth= 3] . ( 2257 sec) [ -46057.1442] [11722] [depth= 1] . ( 2259 sec) [ -46056.6222] [11727] [depth= 1] . ( 2261 sec) [ -46055.7265] [11722] [depth= 1] . ( 2263 sec) [ -46050.7903] [11718] [depth= 1] . ( 2268 sec) [ -46050.5994] [11718] [depth= 1] . ( 2269 sec) [ -46050.4476] [11719] [depth= 1] . ( 2273 sec) [ -46046.3788] [11721] [depth= 2] . ( 2278 sec) [ -46046.1548] [11722] [depth= 1] . ( 2279 sec) [ -46045.4089] [11727] [depth= 1] . ( 2281 sec) [ -46009.3312] [Branch lengths ] . ( 2289 sec) [ -46008.5662] [GTR parameters ] . ( 2289 sec) [ -46008.0436] [Alpha ][ 0.528324] . ( 2290 sec) [ -46007.8876] [11727] [depth= 1] . ( 2313 sec) [ -46007.6337] [11728] [depth= 1] . ( 2324 sec) [ -46007.5380] [11725] [depth= 1] . ( 2367 sec) [ -45992.9999] [Branch lengths ] . ( 2372 sec) [ -45992.7388] [GTR parameters ] . ( 2373 sec) [ -45992.6961] [Alpha ][ 0.531950] . ( 2374 sec) [ -45992.6301] [11725] [depth= 1] . ( 2397 sec) [ -45992.3213] [11729] [depth= 2] . ( 2454 sec) [ -45986.2281] [Branch lengths ] . ( 2461 sec) [ -45986.0998] [GTR parameters ] . ( 2462 sec) [ -45986.0998] [Alpha ][ 0.531950] . ( 2463 sec) [ -45986.0760] [11729] [depth= 1] . ( 2470 sec) [ -45919.5415] [11746] [depth= 14] . ( 2472 sec) [ -45919.0363] [11755] [depth= 1] . ( 2475 sec) [ -45918.5898] [11761] [depth= 1] . ( 2541 sec) [ -45911.9589] [Branch lengths ] . ( 2547 sec) [ -45911.5804] [GTR parameters ] . ( 2547 sec) [ -45911.5450] [Alpha ][ 0.534885] . ( 2557 sec) [ -45911.4020] [11755] [depth= 1] . ( 2626 sec) [ -45908.8496] [Branch lengths ] . ( 2628 sec) [ -45908.8302] [GTR parameters ] . ( 2628 sec) [ -45908.8266] [Alpha ][ 0.535752] . ( 2708 sec) [ -45907.9116] [Branch lengths ] . ( 2712 sec) [ -45906.9405] [11757] [depth= 1] . ( 2726 sec) [ -45901.2874] [11862] [depth= 8] . ( 2736 sec) [ -45898.4243] [11886] [depth= 6] . ( 2749 sec) [ -45897.3031] [11973] [depth= 4] . ( 2762 sec) [ -45896.7487] [11966] [depth= 1] . ( 2787 sec) [ -45896.6851] [11961] [depth= 6] . ( 2815 sec) [ -45896.2109] [11961] [depth= 1] . ( 2897 sec) [ -45894.9374] [11961] [depth= 1] . ( 2924 sec) [ -45894.5000] [11965] [depth= 1] . ( 2929 sec) [ -45894.1600] [11961] [depth= 1] . ( 2933 sec) [ -45892.6795] [11959] [depth= 2] . ( 2961 sec) [ -45884.7326] [Branch lengths ] . ( 2969 sec) [ -45884.4536] [GTR parameters ] . ( 2969 sec) [ -45884.2199] [Alpha ][ 0.527707] . ( 2987 sec) [ -45882.7577] [11965] [depth= 1] . ( 2988 sec) [ -45880.0747] [11939] [depth= 1] . ( 3183 sec) [ -45879.9974] [11943] [depth= 1] . ( 3188 sec) [ -45879.8872] [11939] [depth= 1] . ( 3219 sec) [ -45877.2060] [Branch lengths ] . ( 3224 sec) [ -45877.1917] [GTR parameters ] . ( 3225 sec) [ -45877.1900] [Alpha ][ 0.528410] . ( 3244 sec) [ -45863.9410] [11881] [depth= 3] . ( 3479 sec) [ -45863.0162] [Branch lengths ] . ( 3484 sec) [ -45863.0016] [GTR parameters ] . ( 3485 sec) [ -45862.8792] [Alpha ][ 0.534397] . ( 3502 sec) [ -45862.6956] [11877] [depth= 1] . ( 3739 sec) [ -45862.1857] [Branch lengths ] . ( 3743 sec) [ -45862.1793] [GTR parameters ] . ( 3744 sec) [ -45862.1792] [Alpha ][ 0.535180] . ( 3744 sec) [ -45862.1792] [Topology ] . ( 3750 sec) [ -45862.0868] [Topology ] . ( 3755 sec) [ -45862.0568] [Topology ] . ( 3761 sec) [ -45862.0422] [Topology ] . ( 3766 sec) [ -45862.0343] [Topology ] . ( 3772 sec) [ -45862.0297] [Topology ] . ( 3777 sec) [ -45862.0268] [Topology ] . ( 3779 sec) [ -45862.0263] [GTR parameters ] . ( 3779 sec) [ -45862.0261] [Alpha ][ 0.534645] . ( 3779 sec) [ -45862.0261] [Topology ] . ( 3785 sec) [ -45862.0239] [Topology ] . ( 3790 sec) [ -45862.0225] [Topology ] . ( 3796 sec) [ -45862.0214] [Topology ] . ( 3801 sec) [ -45862.0206] [Topology ] . ( 3803 sec) [ -45862.0200] [GTR parameters ] . ( 3804 sec) [ -45862.0200] [Alpha ][ 0.534645] . ( 3804 sec) [ -45862.0200] [Topology ] . ( 3810 sec) [ -45862.0193] [Topology ] . ( 3811 sec) [ -45862.0193] [GTR parameters ] . ( 3811 sec) [ -45862.0193] [Alpha ][ 0.534645] . Checking for NNIs, optimizing five branches... . ( 3864 sec) [ -45861.8842] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3916 sec) [ -45861.8069] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3968 sec) [ -45861.7437] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4020 sec) [ -45861.0256] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -45996.184860 . Log likelihood obtained after SPR moves : -45861.025631 . Log likelihood of the current tree: -45861.025631. . Printing the most likely tree in file 'nucleic_M2623_139x1044_2006.phy_phyml_tree.txt'... . Time used 1h7m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 4068.08user 0.00system 1:07:56elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps