.......................... 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 : 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 SPR moves)... . ( 4 sec) [ -12577.0498] [GTR parameters ] . ( 4 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 5 sec) [ -12365.3304] [ 2346] [depth= 1] . ( 5 sec) [ -12354.0229] [ 2343] [depth= 2] . ( 6 sec) [ -12353.3959] [ 2342] [depth= 1] . ( 6 sec) [ -12351.9309] [ 2349] [depth= 1] . ( 6 sec) [ -12344.2940] [ 2342] [depth= 1] . ( 7 sec) [ -12343.9370] [ 2345] [depth= 1] . ( 7 sec) [ -12341.1247] [ 2342] [depth= 1] . ( 7 sec) [ -12339.7917] [ 2343] [depth= 1] . ( 7 sec) [ -12330.3304] [ 2338] [depth= 1] . ( 8 sec) [ -12326.8104] [ 2337] [depth= 1] . ( 8 sec) [ -12318.9434] [ 2337] [depth= 1] . ( 8 sec) [ -12317.3269] [ 2336] [depth= 2] . ( 8 sec) [ -12303.1683] [ 2332] [depth= 3] . ( 8 sec) [ -12294.0043] [ 2329] [depth= 1] . ( 9 sec) [ -12291.1314] [ 2326] [depth= 1] . ( 9 sec) [ -12291.1058] [ 2329] [depth= 1] . ( 9 sec) [ -12288.8708] [ 2326] [depth= 1] . ( 10 sec) [ -12286.1366] [ 2329] [depth= 1] . ( 10 sec) [ -12282.5641] [ 2329] [depth= 1] . ( 10 sec) [ -12269.3141] [ 2321] [depth= 2] . ( 10 sec) [ -12263.8640] [ 2319] [depth= 1] . ( 10 sec) [ -12263.1734] [ 2319] [depth= 1] . ( 10 sec) [ -12261.7498] [ 2320] [depth= 2] . ( 11 sec) [ -12248.6114] [ 2317] [depth= 1] . ( 11 sec) [ -12243.9807] [ 2318] [depth= 1] . ( 11 sec) [ -12240.2673] [ 2317] [depth= 1] . ( 11 sec) [ -12238.1635] [ 2317] [depth= 1] . ( 11 sec) [ -12228.9447] [ 2318] [depth= 1] . ( 12 sec) [ -12228.3451] [ 2318] [depth= 1] . ( 12 sec) [ -12225.7493] [ 2316] [depth= 1] . ( 12 sec) [ -12220.5197] [ 2319] [depth= 1] . ( 12 sec) [ -12212.4080] [ 2316] [depth= 7] . ( 13 sec) [ -12209.8607] [ 2318] [depth= 1] . ( 13 sec) [ -12208.6075] [ 2316] [depth= 1] . ( 13 sec) [ -12207.0158] [ 2315] [depth= 1] . ( 13 sec) [ -12192.3979] [ 2311] [depth= 1] . ( 14 sec) [ -12190.7394] [ 2314] [depth= 2] . ( 14 sec) [ -12178.4865] [ 2309] [depth= 2] . ( 14 sec) [ -12177.9119] [ 2308] [depth= 4] . ( 14 sec) [ -12175.6641] [ 2308] [depth= 1] . ( 15 sec) [ -12173.4875] [ 2308] [depth= 1] . ( 15 sec) [ -12173.1418] [ 2308] [depth= 1] . ( 15 sec) [ -12172.8865] [ 2308] [depth= 1] . ( 15 sec) [ -12172.8043] [ 2308] [depth= 1] . ( 15 sec) [ -12172.7810] [ 2308] [depth= 1] . ( 16 sec) [ -12068.8575] [Branch lengths ] . ( 19 sec) [ -12065.5327] [GTR parameters ] . ( 19 sec) [ -12033.6488] [Alpha ][ 0.334589] . ( 21 sec) [ -12033.5335] [ 2309] [depth= 1] . ( 23 sec) [ -12031.0169] [ 2308] [depth= 2] . ( 23 sec) [ -12030.3170] [ 2308] [depth= 2] . ( 24 sec) [ -12027.0210] [ 2312] [depth= 1] . ( 28 sec) [ -12026.4151] [ 2313] [depth= 1] . ( 29 sec) [ -12023.1646] [ 2317] [depth= 8] . ( 30 sec) [ -12020.3120] [ 2321] [depth= 1] . ( 31 sec) [ -12018.2003] [ 2321] [depth= 5] . ( 34 sec) [ -12007.9197] [Branch lengths ] . ( 39 sec) [ -12006.5429] [GTR parameters ] . ( 39 sec) [ -12006.5426] [Alpha ][ 0.334163] . ( 48 sec) [ -12006.2078] [ 2319] [depth= 5] . ( 52 sec) [ -12004.0816] [Branch lengths ] . ( 54 sec) [ -12004.0583] [GTR parameters ] . ( 54 sec) [ -12004.0389] [Alpha ][ 0.337354] . ( 68 sec) [ -12003.5558] [Branch lengths ] . ( 177 sec) [ -12003.4630] [Branch lengths ] . ( 177 sec) [ -12003.4630] [Topology ] . ( 179 sec) [ -12002.3183] [Topology ] . ( 182 sec) [ -12002.0889] [Topology ] . ( 185 sec) [ -12002.0680] [Topology ] . ( 188 sec) [ -12002.0637] [Topology ] . ( 190 sec) [ -12002.0626] [Topology ] . ( 193 sec) [ -12002.0622] [Topology ] . ( 195 sec) [ -12002.0349] [GTR parameters ] . ( 195 sec) [ -12002.0277] [Alpha ][ 0.339281] . ( 195 sec) [ -12002.0277] [Topology ] . ( 198 sec) [ -12002.0267] [Topology ] . ( 201 sec) [ -12002.0262] [Topology ] . ( 201 sec) [ -12002.0262] [GTR parameters ] . ( 201 sec) [ -12002.0262] [Alpha ][ 0.339281] . ( 202 sec) [ -12002.0262] [Topology ] . ( 204 sec) [ -12002.0260] [Topology ] . ( 205 sec) [ -12002.0260] [GTR parameters ] . ( 205 sec) [ -12002.0260] [Alpha ][ 0.339281] . Checking for NNIs, optimizing five branches... . ( 224 sec) [ -12001.9834] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12001.983387. . Printing the most likely tree in file 'nucleic_M2566_73x918_2006.phy_phyml_tree.txt'... . Time used 0h4m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 166.69user 0.00system 4:04.98elapsed 68%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps