.......................... 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 ] . ( 5 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 13 sec) [ -12372.0910] [ 2346] [depth= 1] . ( 19 sec) [ -12365.6601] [ 2339] [depth= 1] . ( 19 sec) [ -12348.5829] [ 2331] [depth= 3] . ( 19 sec) [ -12347.6174] [ 2337] [depth= 1] . ( 21 sec) [ -12336.0076] [ 2335] [depth= 2] . ( 22 sec) [ -12335.3439] [ 2334] [depth= 1] . ( 30 sec) [ -12333.0538] [ 2341] [depth= 1] . ( 30 sec) [ -12325.5847] [ 2334] [depth= 1] . ( 37 sec) [ -12325.5448] [ 2336] [depth= 1] . ( 37 sec) [ -12324.2843] [ 2339] [depth= 1] . ( 38 sec) [ -12321.8725] [ 2336] [depth= 1] . ( 45 sec) [ -12320.6160] [ 2337] [depth= 1] . ( 49 sec) [ -12318.4430] [ 2335] [depth= 1] . ( 49 sec) [ -12318.1016] [ 2337] [depth= 1] . ( 49 sec) [ -12317.9179] [ 2339] [depth= 1] . ( 51 sec) [ -12314.8364] [ 2339] [depth= 1] . ( 51 sec) [ -12307.5048] [ 2339] [depth= 1] . ( 51 sec) [ -12304.4437] [ 2337] [depth= 1] . ( 55 sec) [ -12304.1175] [ 2337] [depth= 2] . ( 55 sec) [ -12303.1872] [ 2335] [depth= 1] . ( 55 sec) [ -12300.7150] [ 2339] [depth= 4] . ( 55 sec) [ -12298.4712] [ 2339] [depth= 1] . ( 55 sec) [ -12293.8693] [ 2339] [depth= 1] . ( 73 sec) [ -12290.6691] [ 2336] [depth= 1] . ( 75 sec) [ -12289.7558] [ 2339] [depth= 1] . ( 76 sec) [ -12285.9640] [ 2346] [depth= 1] . ( 79 sec) [ -12283.4019] [ 2350] [depth= 1] . ( 79 sec) [ -12269.9404] [ 2346] [depth= 1] . ( 79 sec) [ -12265.7413] [ 2346] [depth= 1] . ( 79 sec) [ -12252.1808] [ 2338] [depth= 2] . ( 79 sec) [ -12244.7562] [ 2336] [depth= 1] . ( 79 sec) [ -12243.4019] [ 2337] [depth= 2] . ( 82 sec) [ -12243.1507] [ 2337] [depth= 1] . ( 82 sec) [ -12241.8591] [ 2336] [depth= 2] . ( 83 sec) [ -12230.6217] [ 2335] [depth= 1] . ( 85 sec) [ -12225.0665] [ 2336] [depth= 1] . ( 85 sec) [ -12221.0196] [ 2335] [depth= 1] . ( 85 sec) [ -12219.6637] [ 2334] [depth= 2] . ( 85 sec) [ -12209.9578] [ 2330] [depth= 3] . ( 85 sec) [ -12208.0980] [ 2324] [depth= 1] . ( 85 sec) [ -12207.7510] [ 2325] [depth= 1] . ( 85 sec) [ -12200.8352] [ 2324] [depth= 1] . ( 94 sec) [ -12189.6633] [ 2322] [depth= 1] . ( 98 sec) [ -12188.5074] [ 2321] [depth= 1] . ( 102 sec) [ -12186.3498] [ 2318] [depth= 3] . ( 117 sec) [ -12186.2105] [ 2320] [depth= 1] . ( 124 sec) [ -12185.6404] [ 2320] [depth= 1] . ( 124 sec) [ -12177.7243] [ 2320] [depth= 1] . ( 125 sec) [ -12177.3022] [ 2321] [depth= 1] . ( 127 sec) [ -12176.6602] [ 2320] [depth= 1] . ( 127 sec) [ -12173.3269] [ 2323] [depth= 2] . ( 128 sec) [ -12162.1844] [ 2318] [depth= 2] . ( 129 sec) [ -12162.1042] [ 2317] [depth= 4] . ( 129 sec) [ -12159.9834] [ 2317] [depth= 1] . ( 135 sec) [ -12157.7656] [ 2317] [depth= 1] . ( 136 sec) [ -12157.4305] [ 2317] [depth= 1] . ( 136 sec) [ -12157.1417] [ 2317] [depth= 1] . ( 137 sec) [ -12157.0598] [ 2317] [depth= 1] . ( 138 sec) [ -12157.0368] [ 2317] [depth= 1] . ( 148 sec) [ -12055.5145] [Branch lengths ] . ( 151 sec) [ -12051.7485] [GTR parameters ] . ( 151 sec) [ -12018.6844] [Alpha ][ 0.334138] . ( 172 sec) [ -12018.5591] [ 2318] [depth= 1] . ( 186 sec) [ -12017.9984] [ 2315] [depth= 1] . ( 205 sec) [ -12017.0928] [ 2318] [depth= 2] . ( 238 sec) [ -12016.8152] [ 2315] [depth= 1] . ( 265 sec) [ -12016.4451] [ 2322] [depth= 1] . ( 265 sec) [ -12015.2418] [ 2321] [depth= 1] . ( 269 sec) [ -12014.1671] [ 2323] [depth= 1] . ( 282 sec) [ -12013.9613] [ 2314] [depth= 1] . ( 313 sec) [ -12012.1305] [ 2314] [depth= 5] . ( 338 sec) [ -12004.7188] [Branch lengths ] . ( 340 sec) [ -12004.1675] [GTR parameters ] . ( 340 sec) [ -12004.1643] [Alpha ][ 0.335400] . ( 405 sec) [ -12003.3049] [ 2314] [depth= 2] . ( 536 sec) [ -12001.5466] [Branch lengths ] . ( 538 sec) [ -12001.5253] [GTR parameters ] . ( 538 sec) [ -12001.5208] [Alpha ][ 0.336897] . ( 733 sec) [ -12001.2879] [Branch lengths ] . ( 807 sec) [ -12001.2540] [Branch lengths ] . ( 807 sec) [ -12001.2540] [Topology ] . ( 809 sec) [ -12001.1390] [Topology ] . ( 811 sec) [ -12001.0175] [Topology ] . ( 813 sec) [ -12001.0104] [Topology ] . ( 814 sec) [ -12001.0088] [Topology ] . ( 816 sec) [ -12001.0083] [Topology ] . ( 818 sec) [ -12001.0007] [GTR parameters ] . ( 818 sec) [ -12000.9987] [Alpha ][ 0.337882] . ( 818 sec) [ -12000.9987] [Topology ] . ( 820 sec) [ -12000.9980] [Topology ] . ( 820 sec) [ -12000.9980] [GTR parameters ] . ( 821 sec) [ -12000.9980] [Alpha ][ 0.337882] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12000.997986. . Printing the most likely tree in file 'nucleic_M2566_73x918_2006.phy_phyml_tree.txt'... . Time used 0h13m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 824.97user 0.00system 13:54.26elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps