.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2566_73x918_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 541 patterns found. (out of a total of 918 sites) . 442 sites without polymorphism (48.15%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -12577.0498] [GTR parameters ] . ( 5 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 5 sec) [ -12377.0948] [Topology ] . ( 6 sec) [ -12129.6581] [Topology ] . ( 8 sec) [ -12077.7104] [Topology ] . ( 10 sec) [ -12066.1739] [Topology ] . ( 12 sec) [ -12059.8968] [Topology ] . ( 13 sec) [ -12056.6268] [Topology ] . ( 15 sec) [ -12055.4653] [Topology ] . ( 17 sec) [ -12055.0915] [Topology ] . ( 19 sec) [ -12054.9395] [Topology ] . ( 20 sec) [ -12054.8734] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -12049.4145] [GTR parameters ] . ( 39 sec) [ -12019.0259] [Alpha ][ 0.342808] . ( 39 sec) [ -12019.0259] [Topology ] . ( 41 sec) [ -12018.5158] [Topology ] . ( 42 sec) [ -12018.4764] [Topology ] . ( 44 sec) [ -12018.4681] [Topology ] . ( 46 sec) [ -12018.4656] [Topology ] . ( 48 sec) [ -12018.4647] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -12018.2149] [GTR parameters ] . ( 63 sec) [ -12018.2002] [Alpha ][ 0.339937] . ( 63 sec) [ -12018.2002] [Topology ] . ( 64 sec) [ -12018.1950] [Topology ] . ( 66 sec) [ -12018.1935] [Topology ] . ( 68 sec) [ -12018.1928] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -12018.1923] [GTR parameters ] . ( 81 sec) [ -12018.1923] [Alpha ][ 0.340277] . ( 81 sec) [ -12018.1923] [Topology ] . ( 83 sec) [ -12018.1918] [Topology ] . Checking for NNIs, optimizing five branches... . ( 96 sec) [ -12018.1918] [GTR parameters ] . ( 96 sec) [ -12018.1918] [Alpha ][ 0.340277] . ( 96 sec) [ -12018.1918] [Topology ] . ( 98 sec) [ -12018.1916] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 128 sec) [ -12577.0498] [GTR parameters ] . ( 128 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 129 sec) [ -12365.3304] [ 2346] [depth= 1] . ( 129 sec) [ -12354.0229] [ 2343] [depth= 2] . ( 129 sec) [ -12353.3959] [ 2342] [depth= 1] . ( 130 sec) [ -12351.9309] [ 2349] [depth= 1] . ( 130 sec) [ -12344.2940] [ 2342] [depth= 1] . ( 131 sec) [ -12343.9370] [ 2345] [depth= 1] . ( 131 sec) [ -12341.1247] [ 2342] [depth= 1] . ( 131 sec) [ -12339.7917] [ 2343] [depth= 1] . ( 132 sec) [ -12330.3304] [ 2338] [depth= 1] . ( 132 sec) [ -12326.8104] [ 2337] [depth= 1] . ( 132 sec) [ -12318.9434] [ 2337] [depth= 1] . ( 133 sec) [ -12317.3269] [ 2336] [depth= 2] . ( 133 sec) [ -12315.1793] [ 2341] [depth= 1] . ( 133 sec) [ -12302.5428] [ 2333] [depth= 3] . ( 133 sec) [ -12295.8939] [ 2330] [depth= 1] . ( 133 sec) [ -12285.8561] [ 2329] [depth= 1] . ( 134 sec) [ -12282.8796] [ 2326] [depth= 1] . ( 134 sec) [ -12282.8441] [ 2330] [depth= 1] . ( 135 sec) [ -12278.1742] [ 2333] [depth= 1] . ( 135 sec) [ -12266.9658] [ 2330] [depth= 1] . ( 135 sec) [ -12263.0264] [ 2330] [depth= 1] . ( 135 sec) [ -12249.6816] [ 2322] [depth= 2] . ( 135 sec) [ -12244.2880] [ 2320] [depth= 1] . ( 136 sec) [ -12243.7901] [ 2320] [depth= 1] . ( 136 sec) [ -12242.3925] [ 2321] [depth= 2] . ( 136 sec) [ -12229.5147] [ 2323] [depth= 1] . ( 136 sec) [ -12224.1700] [ 2324] [depth= 1] . ( 136 sec) [ -12220.4438] [ 2323] [depth= 1] . ( 137 sec) [ -12218.3062] [ 2323] [depth= 1] . ( 137 sec) [ -12209.6820] [ 2324] [depth= 1] . ( 137 sec) [ -12207.7561] [ 2320] [depth= 1] . ( 137 sec) [ -12207.2951] [ 2319] [depth= 1] . ( 138 sec) [ -12204.6151] [ 2318] [depth= 1] . ( 138 sec) [ -12199.8629] [ 2319] [depth= 1] . ( 138 sec) [ -12196.1650] [ 2320] [depth= 5] . ( 139 sec) [ -12193.7131] [ 2323] [depth= 1] . ( 139 sec) [ -12185.3317] [ 2319] [depth= 1] . ( 139 sec) [ -12185.1923] [ 2324] [depth= 1] . ( 140 sec) [ -12178.7280] [ 2328] [depth= 1] . ( 140 sec) [ -12178.1013] [ 2329] [depth= 1] . ( 140 sec) [ -12176.5338] [ 2330] [depth= 1] . ( 140 sec) [ -12171.8305] [ 2329] [depth= 1] . ( 141 sec) [ -12170.4235] [ 2324] [depth= 1] . ( 141 sec) [ -12160.5764] [ 2321] [depth= 1] . ( 141 sec) [ -12157.6967] [ 2321] [depth= 1] . ( 142 sec) [ -12157.3158] [ 2320] [depth= 4] . ( 142 sec) [ -12156.8007] [ 2320] [depth= 1] . ( 142 sec) [ -12156.4817] [ 2320] [depth= 1] . ( 143 sec) [ -12156.4257] [ 2320] [depth= 1] . ( 145 sec) [ -12066.3627] [Branch lengths ] . ( 147 sec) [ -12061.7387] [GTR parameters ] . ( 147 sec) [ -12029.8111] [Alpha ][ 0.335117] . ( 149 sec) [ -12029.7924] [ 2321] [depth= 1] . ( 151 sec) [ -12028.6586] [ 2321] [depth= 2] . ( 152 sec) [ -12027.8434] [ 2322] [depth= 2] . ( 152 sec) [ -12027.4406] [ 2311] [depth= 2] . ( 155 sec) [ -12025.2256] [ 2313] [depth= 1] . ( 155 sec) [ -12024.1298] [ 2314] [depth= 1] . ( 156 sec) [ -12023.3466] [ 2317] [depth= 8] . ( 157 sec) [ -12022.5281] [ 2318] [depth= 1] . ( 159 sec) [ -12020.5984] [ 2318] [depth= 5] . ( 163 sec) [ -12004.6389] [Branch lengths ] . ( 165 sec) [ -12004.1797] [GTR parameters ] . ( 165 sec) [ -12004.1775] [Alpha ][ 0.336180] . ( 171 sec) [ -12004.1566] [ 2319] [depth= 1] . ( 185 sec) [ -12002.2446] [Branch lengths ] . ( 187 sec) [ -12002.2318] [GTR parameters ] . ( 187 sec) [ -12002.2282] [Alpha ][ 0.337511] . ( 207 sec) [ -12002.0719] [Branch lengths ] . ( 284 sec) [ -12002.0517] [Branch lengths ] . ( 284 sec) [ -12002.0517] [Topology ] . ( 286 sec) [ -12001.1336] [Topology ] . ( 287 sec) [ -12001.0186] [Topology ] . ( 289 sec) [ -12001.0091] [Topology ] . ( 291 sec) [ -12001.0076] [Topology ] . ( 293 sec) [ -12001.0073] [Topology ] . ( 295 sec) [ -12000.9981] [GTR parameters ] . ( 295 sec) [ -12000.9977] [Alpha ][ 0.337953] . ( 295 sec) [ -12000.9977] [Topology ] . ( 297 sec) [ -12000.9974] [Topology ] . ( 297 sec) [ -12000.9974] [GTR parameters ] . ( 297 sec) [ -12000.9974] [Alpha ][ 0.337953] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12018.191571 . Log likelihood obtained after SPR moves : -12000.997416 . Log likelihood of the current tree: -12000.997416. . Printing the most likely tree in file 'nucleic_M2566_73x918_2006.phy_phyml_tree.txt'... . Time used 0h5m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 309.77user 0.00system 5:10.90elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps