.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -8163.5103] [GTR parameters ] . ( 3 sec) [ -8080.4464] [Alpha ][ 0.500960] . ( 4 sec) [ -8077.4988] [ 943] [depth= 1] . ( 4 sec) [ -8074.4226] [ 944] [depth= 1] . ( 5 sec) [ -8069.8592] [ 943] [depth= 1] . ( 5 sec) [ -8065.7549] [ 943] [depth= 2] . ( 5 sec) [ -8035.2996] [ 934] [depth= 12] . ( 5 sec) [ -8035.0145] [ 934] [depth= 1] . ( 5 sec) [ -8033.2509] [ 934] [depth= 1] . ( 5 sec) [ -8032.7544] [ 934] [depth= 1] . ( 5 sec) [ -8032.5127] [ 934] [depth= 2] . ( 5 sec) [ -8030.9011] [ 932] [depth= 1] . ( 6 sec) [ -8030.4313] [ 932] [depth= 2] . ( 6 sec) [ -8017.8924] [ 929] [depth= 3] . ( 6 sec) [ -8013.1719] [ 928] [depth= 1] . ( 7 sec) [ -8003.6892] [ 924] [depth= 3] . ( 7 sec) [ -7995.0424] [ 922] [depth= 3] . ( 7 sec) [ -7988.9344] [ 922] [depth= 3] . ( 7 sec) [ -7978.0168] [ 918] [depth= 1] . ( 7 sec) [ -7975.5995] [ 919] [depth= 1] . ( 8 sec) [ -7964.9049] [ 920] [depth= 2] . ( 8 sec) [ -7958.0851] [ 918] [depth= 1] . ( 8 sec) [ -7948.9211] [ 915] [depth= 6] . ( 8 sec) [ -7948.0876] [ 915] [depth= 1] . ( 8 sec) [ -7946.1442] [ 915] [depth= 2] . ( 9 sec) [ -7943.6702] [ 915] [depth= 3] . ( 9 sec) [ -7939.4656] [ 914] [depth= 2] . ( 9 sec) [ -7939.3166] [ 914] [depth= 2] . ( 9 sec) [ -7939.3045] [ 914] [depth= 2] . ( 9 sec) [ -7938.5169] [ 914] [depth= 1] . ( 9 sec) [ -7938.0549] [ 914] [depth= 2] . ( 10 sec) [ -7937.8506] [ 914] [depth= 4] . ( 10 sec) [ -7937.4781] [ 914] [depth= 5] . ( 10 sec) [ -7936.4782] [ 914] [depth= 1] . ( 10 sec) [ -7935.7099] [ 914] [depth= 2] . ( 10 sec) [ -7933.6185] [ 913] [depth= 6] . ( 10 sec) [ -7931.9011] [ 913] [depth= 1] . ( 10 sec) [ -7926.1273] [ 911] [depth= 4] . ( 10 sec) [ -7922.5860] [ 911] [depth= 1] . ( 11 sec) [ -7920.1428] [ 911] [depth= 3] . ( 11 sec) [ -7919.8774] [ 911] [depth= 1] . ( 11 sec) [ -7917.2575] [ 912] [depth= 11] . ( 11 sec) [ -7916.8684] [ 910] [depth= 2] . ( 11 sec) [ -7916.0098] [ 910] [depth= 1] . ( 11 sec) [ -7915.9048] [ 910] [depth= 1] . ( 12 sec) [ -7915.5774] [ 910] [depth= 1] . ( 12 sec) [ -7915.4243] [ 910] [depth= 1] . ( 12 sec) [ -7915.3137] [ 910] [depth= 2] . ( 12 sec) [ -7891.3239] [Branch lengths ] . ( 15 sec) [ -7890.9520] [GTR parameters ] . ( 15 sec) [ -7844.1183] [Alpha ][ 0.250961] . ( 15 sec) [ -7842.7332] [ 911] [depth= 1] . ( 16 sec) [ -7841.2012] [ 910] [depth= 5] . ( 17 sec) [ -7841.1369] [ 910] [depth= 1] . ( 17 sec) [ -7841.1190] [ 910] [depth= 1] . ( 19 sec) [ -7840.8929] [ 910] [depth= 1] . ( 19 sec) [ -7838.9769] [ 909] [depth= 4] . ( 20 sec) [ -7838.9035] [ 909] [depth= 1] . ( 21 sec) [ -7838.4937] [ 909] [depth= 1] . ( 21 sec) [ -7838.4713] [ 909] [depth= 1] . ( 22 sec) [ -7838.4498] [ 909] [depth= 2] . ( 22 sec) [ -7838.4239] [ 909] [depth= 3] . ( 22 sec) [ -7838.3748] [ 909] [depth= 1] . ( 25 sec) [ -7832.9975] [Branch lengths ] . ( 27 sec) [ -7832.9867] [GTR parameters ] . ( 27 sec) [ -7830.9252] [Alpha ][ 0.213014] . ( 32 sec) [ -7830.7936] [ 909] [depth= 1] . ( 33 sec) [ -7830.7834] [ 909] [depth= 1] . ( 37 sec) [ -7830.6465] [Branch lengths ] . ( 38 sec) [ -7830.6400] [GTR parameters ] . ( 39 sec) [ -7830.6396] [Alpha ][ 0.212473] . ( 68 sec) [ -7828.8271] [ 911] [depth= 2] . ( 105 sec) [ -7828.4334] [ 911] [depth= 1] . ( 112 sec) [ -7828.2557] [Branch lengths ] . ( 114 sec) [ -7828.2151] [GTR parameters ] . ( 114 sec) [ -7828.2151] [Alpha ][ 0.212473] . ( 213 sec) [ -7828.2104] [Branch lengths ] . ( 213 sec) [ -7828.2104] [Topology ] . ( 216 sec) [ -7828.2101] [Topology ] . ( 217 sec) [ -7828.2100] [GTR parameters ] . ( 217 sec) [ -7828.2098] [Alpha ][ 0.212741] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -7828.2075] [Topology ] . Checking for NNIs, optimizing five branches... . ( 257 sec) [ -7828.1403] [Topology ] . Checking for NNIs, optimizing five branches... . ( 277 sec) [ -7828.1385] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7828.138550. . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Time used 0h4m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 229.77user 0.00system 4:58.39elapsed 77%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps