.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2845_68x1715_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 649 patterns found. (out of a total of 1715 sites) . 1119 sites without polymorphism (65.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -11816.7722] [GTR parameters ] . ( 5 sec) [ -11662.0849] [Alpha ][ 0.500960] . ( 5 sec) [ -11662.0849] [Topology ] . ( 7 sec) [ -11513.5370] [Topology ] . ( 9 sec) [ -11479.6099] [Topology ] . ( 11 sec) [ -11468.4331] [Topology ] . ( 13 sec) [ -11460.4879] [Topology ] . ( 15 sec) [ -11454.4989] [Topology ] . ( 17 sec) [ -11448.0247] [Topology ] . ( 19 sec) [ -11444.6531] [Topology ] . ( 21 sec) [ -11443.4847] [Topology ] . ( 23 sec) [ -11443.3898] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -11443.1080] [Topology ] . ( 42 sec) [ -11441.9514] [GTR parameters ] . ( 42 sec) [ -11364.0125] [Alpha ][ 0.254613] . ( 42 sec) [ -11364.0125] [Topology ] . ( 44 sec) [ -11362.8246] [Topology ] . ( 46 sec) [ -11362.2598] [Topology ] . ( 48 sec) [ -11361.9487] [Topology ] . ( 50 sec) [ -11361.7736] [Topology ] . ( 52 sec) [ -11361.6743] [Topology ] . ( 54 sec) [ -11361.6180] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -11361.4064] [GTR parameters ] . ( 70 sec) [ -11361.4060] [Alpha ][ 0.254194] . ( 70 sec) [ -11361.4060] [Topology ] . ( 72 sec) [ -11361.3635] [Topology ] . ( 74 sec) [ -11361.3397] [Topology ] . ( 76 sec) [ -11361.3261] [Topology ] . ( 78 sec) [ -11361.3184] [Topology ] . ( 80 sec) [ -11361.3140] [Topology ] . ( 82 sec) [ -11361.3114] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -11361.3108] [GTR parameters ] . ( 97 sec) [ -11361.3108] [Alpha ][ 0.254194] . ( 97 sec) [ -11361.3108] [Topology ] . ( 99 sec) [ -11361.3092] [Topology ] . ( 101 sec) [ -11361.3083] [Topology ] . Checking for NNIs, optimizing five branches... . ( 115 sec) [ -11361.3083] [GTR parameters ] . ( 115 sec) [ -11361.3083] [Alpha ][ 0.254194] . ( 116 sec) [ -11361.3083] [Topology ] . ( 118 sec) [ -11361.3078] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 151 sec) [ -11816.7722] [GTR parameters ] . ( 151 sec) [ -11662.0849] [Alpha ][ 0.500960] . ( 151 sec) [ -11660.9342] [ 1610] [depth= 1] . ( 152 sec) [ -11660.7720] [ 1610] [depth= 1] . ( 152 sec) [ -11660.6848] [ 1610] [depth= 1] . ( 152 sec) [ -11660.5983] [ 1610] [depth= 1] . ( 152 sec) [ -11660.4280] [ 1610] [depth= 1] . ( 153 sec) [ -11659.1195] [ 1610] [depth= 1] . ( 153 sec) [ -11655.5792] [ 1610] [depth= 1] . ( 153 sec) [ -11653.6958] [ 1610] [depth= 1] . ( 154 sec) [ -11653.5560] [ 1617] [depth= 1] . ( 154 sec) [ -11647.5359] [ 1616] [depth= 1] . ( 155 sec) [ -11646.9829] [ 1618] [depth= 1] . ( 155 sec) [ -11645.8122] [ 1616] [depth= 1] . ( 155 sec) [ -11645.5713] [ 1616] [depth= 3] . ( 155 sec) [ -11642.9865] [ 1615] [depth= 2] . ( 155 sec) [ -11639.1255] [ 1615] [depth= 2] . ( 155 sec) [ -11631.4518] [ 1613] [depth= 1] . ( 155 sec) [ -11630.4177] [ 1613] [depth= 1] . ( 155 sec) [ -11629.4935] [ 1614] [depth= 1] . ( 156 sec) [ -11624.7814] [ 1609] [depth= 1] . ( 156 sec) [ -11624.2745] [ 1608] [depth= 1] . ( 156 sec) [ -11615.9658] [ 1607] [depth= 1] . ( 156 sec) [ -11614.0316] [ 1606] [depth= 1] . ( 156 sec) [ -11611.2085] [ 1605] [depth= 1] . ( 157 sec) [ -11608.8003] [ 1605] [depth= 2] . ( 157 sec) [ -11604.5634] [ 1604] [depth= 1] . ( 157 sec) [ -11603.2791] [ 1603] [depth= 2] . ( 157 sec) [ -11601.4508] [ 1604] [depth= 1] . ( 158 sec) [ -11599.4456] [ 1603] [depth= 1] . ( 158 sec) [ -11593.9885] [ 1602] [depth= 1] . ( 159 sec) [ -11593.7677] [ 1603] [depth= 1] . ( 159 sec) [ -11592.7014] [ 1602] [depth= 1] . ( 159 sec) [ -11590.9106] [ 1603] [depth= 1] . ( 160 sec) [ -11588.4466] [ 1602] [depth= 1] . ( 160 sec) [ -11585.1893] [ 1603] [depth= 1] . ( 161 sec) [ -11584.6804] [ 1605] [depth= 2] . ( 161 sec) [ -11580.7398] [ 1604] [depth= 1] . ( 161 sec) [ -11577.4276] [ 1602] [depth= 1] . ( 162 sec) [ -11576.4872] [ 1604] [depth= 1] . ( 162 sec) [ -11569.0564] [ 1602] [depth= 1] . ( 162 sec) [ -11557.9330] [ 1602] [depth= 1] . ( 164 sec) [ -11556.8586] [ 1603] [depth= 1] . ( 164 sec) [ -11554.2881] [ 1602] [depth= 1] . ( 164 sec) [ -11553.8444] [ 1603] [depth= 2] . ( 164 sec) [ -11552.7902] [ 1602] [depth= 1] . ( 165 sec) [ -11552.7192] [ 1603] [depth= 1] . ( 165 sec) [ -11549.1910] [ 1607] [depth= 1] . ( 165 sec) [ -11548.8773] [ 1609] [depth= 1] . ( 165 sec) [ -11548.2278] [ 1606] [depth= 2] . ( 166 sec) [ -11547.0035] [ 1605] [depth= 2] . ( 166 sec) [ -11544.2710] [ 1602] [depth= 1] . ( 166 sec) [ -11542.9243] [ 1602] [depth= 1] . ( 166 sec) [ -11542.7269] [ 1602] [depth= 1] . ( 167 sec) [ -11541.4706] [ 1601] [depth= 1] . ( 167 sec) [ -11541.3664] [ 1603] [depth= 2] . ( 167 sec) [ -11541.3481] [ 1601] [depth= 2] . ( 167 sec) [ -11538.7603] [ 1601] [depth= 1] . ( 167 sec) [ -11536.8803] [ 1602] [depth= 1] . ( 168 sec) [ -11536.0622] [ 1603] [depth= 1] . ( 168 sec) [ -11531.8166] [ 1605] [depth= 1] . ( 169 sec) [ -11531.0573] [ 1604] [depth= 1] . ( 170 sec) [ -11473.7781] [Branch lengths ] . ( 173 sec) [ -11472.9610] [GTR parameters ] . ( 173 sec) [ -11396.0721] [Alpha ][ 0.250755] . ( 173 sec) [ -11394.9082] [ 1604] [depth= 1] . ( 174 sec) [ -11394.8949] [ 1604] [depth= 1] . ( 174 sec) [ -11388.7926] [ 1597] [depth= 1] . ( 174 sec) [ -11388.4168] [ 1598] [depth= 2] . ( 175 sec) [ -11388.4015] [ 1598] [depth= 1] . ( 175 sec) [ -11388.2976] [ 1598] [depth= 1] . ( 175 sec) [ -11388.0823] [ 1597] [depth= 1] . ( 176 sec) [ -11387.4957] [ 1598] [depth= 1] . ( 176 sec) [ -11385.9593] [ 1597] [depth= 1] . ( 183 sec) [ -11383.9251] [ 1593] [depth= 2] . ( 183 sec) [ -11381.9572] [ 1594] [depth= 1] . ( 185 sec) [ -11381.8798] [ 1596] [depth= 1] . ( 186 sec) [ -11380.8797] [ 1596] [depth= 1] . ( 187 sec) [ -11380.5844] [ 1595] [depth= 1] . ( 188 sec) [ -11380.1731] [ 1593] [depth= 1] . ( 189 sec) [ -11379.4205] [ 1592] [depth= 2] . ( 190 sec) [ -11376.4039] [ 1591] [depth= 3] . ( 191 sec) [ -11375.7895] [ 1591] [depth= 1] . ( 191 sec) [ -11375.2708] [ 1591] [depth= 2] . ( 192 sec) [ -11374.0964] [ 1591] [depth= 1] . ( 193 sec) [ -11372.7319] [ 1591] [depth= 1] . ( 194 sec) [ -11360.7021] [Branch lengths ] . ( 196 sec) [ -11360.3432] [GTR parameters ] . ( 196 sec) [ -11360.3110] [Alpha ][ 0.253994] . ( 198 sec) [ -11360.2823] [ 1591] [depth= 1] . ( 221 sec) [ -11358.6957] [Branch lengths ] . ( 222 sec) [ -11358.6920] [GTR parameters ] . ( 222 sec) [ -11358.6920] [Alpha ][ 0.254247] . ( 245 sec) [ -11358.3436] [Branch lengths ] . ( 324 sec) [ -11358.2721] [Branch lengths ] . ( 325 sec) [ -11358.2721] [Topology ] . ( 327 sec) [ -11358.1921] [Topology ] . ( 329 sec) [ -11358.1054] [Topology ] . ( 331 sec) [ -11358.0932] [Topology ] . ( 332 sec) [ -11358.0893] [Topology ] . ( 334 sec) [ -11358.0875] [Topology ] . ( 336 sec) [ -11358.0866] [Topology ] . ( 339 sec) [ -11358.0798] [GTR parameters ] . ( 339 sec) [ -11358.0798] [Alpha ][ 0.254247] . ( 339 sec) [ -11358.0798] [Topology ] . ( 341 sec) [ -11358.0790] [Topology ] . ( 341 sec) [ -11358.0790] [GTR parameters ] . ( 342 sec) [ -11358.0790] [Alpha ][ 0.254247] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11361.307799 . Log likelihood obtained after SPR moves : -11358.079001 . Log likelihood of the current tree: -11358.079001. . Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'... . Time used 0h5m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 354.47user 0.00system 5:57.27elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps