.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data77.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 . Compressing sequences... . 366 patterns found. (out of a total of 500 sites) . 115 sites without polymorphism (23.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6837.014629 . ( 1 sec) [ -6833.8334] [GTR parameters ] . ( 1 sec) [ -6833.8144] [Alpha ][ 0.982107] . ( 1 sec) [ -6833.8144] [Topology ] . ( 2 sec) [ -6783.5166] [Topology ] . ( 2 sec) [ -6777.4126] [Topology ] . ( 3 sec) [ -6775.8797] [Topology ] . ( 4 sec) [ -6775.4011] [Topology ] . ( 5 sec) [ -6775.2451] [Topology ] . ( 5 sec) [ -6775.1839] [Topology ] . ( 6 sec) [ -6775.1560] [Topology ] . ( 7 sec) [ -6775.1420] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6775.141959 . ( 12 sec) [ -6775.0278] [GTR parameters ] . ( 12 sec) [ -6775.0088] [Alpha ][ 0.965434] . ( 12 sec) [ -6775.0088] [Topology ] . ( 13 sec) [ -6774.9993] [Topology ] . ( 14 sec) [ -6774.9942] [Topology ] . ( 14 sec) [ -6774.9913] [Topology ] . ( 15 sec) [ -6774.9894] [Topology ] . ( 16 sec) [ -6774.9882] [Topology ] . ( 16 sec) [ -6774.9874] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6774.987441 . ( 22 sec) [ -6774.9873] [GTR parameters ] . ( 22 sec) [ -6774.9871] [Alpha ][ 0.963721] . ( 22 sec) [ -6774.9871] [Topology ] . ( 23 sec) [ -6774.9866] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 34 sec) [ -6833.8334] [GTR parameters ] . ( 34 sec) [ -6833.8144] [Alpha ][ 0.982107] . ( 34 sec) [ -6830.9359] [ 1313] [depth= 1] . ( 34 sec) [ -6830.0693] [ 1314] [depth= 1] . ( 34 sec) [ -6829.7740] [ 1314] [depth= 1] . ( 34 sec) [ -6829.6858] [ 1314] [depth= 1] . ( 35 sec) [ -6814.8557] [ 1306] [depth= 2] . ( 35 sec) [ -6810.4107] [ 1305] [depth= 1] . ( 35 sec) [ -6809.3828] [ 1308] [depth= 2] . ( 35 sec) [ -6806.3070] [ 1306] [depth= 2] . ( 35 sec) [ -6802.4797] [ 1306] [depth= 1] . ( 36 sec) [ -6792.7187] [ 1313] [depth= 1] . ( 36 sec) [ -6792.0049] [ 1316] [depth= 1] . ( 36 sec) [ -6791.6811] [ 1306] [depth= 1] . ( 36 sec) [ -6790.5318] [ 1307] [depth= 1] . ( 36 sec) [ -6788.5633] [ 1306] [depth= 1] . ( 37 sec) [ -6786.7439] [ 1307] [depth= 1] . ( 37 sec) [ -6786.5418] [ 1306] [depth= 1] . ( 37 sec) [ -6777.0457] [Branch lengths ] . ( 38 sec) [ -6776.9573] [GTR parameters ] . ( 38 sec) [ -6776.9457] [Alpha ][ 0.969161] . ( 38 sec) [ -6776.9073] [ 1306] [depth= 1] . ( 38 sec) [ -6776.8669] [ 1306] [depth= 1] . ( 40 sec) [ -6776.2575] [ 1307] [depth= 1] . ( 41 sec) [ -6775.1132] [Branch lengths ] . ( 41 sec) [ -6775.1096] [GTR parameters ] . ( 41 sec) [ -6775.1065] [Alpha ][ 0.961965] . ( 45 sec) [ -6775.0538] [Branch lengths ] . ( 66 sec) [ -6775.0487] [Branch lengths ] . ( 66 sec) [ -6775.0487] [Topology ] . ( 67 sec) [ -6775.0482] [Topology ] . ( 67 sec) [ -6775.0481] [GTR parameters ] . ( 67 sec) [ -6775.0480] [Alpha ][ 0.962927] . Checking for NNIs, optimizing five branches... . ( 72 sec) [ -6774.9873] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6774.986552 . Log likelihood obtained after SPR moves : -6774.987290 . Log likelihood of the current tree: -6774.986552. . Printing the most likely tree in file 'data77.phy_phyml_tree.txt'... . Time used 0h1m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo