.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data39.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... . 451 patterns found. (out of a total of 500 sites) . 50 sites without polymorphism (10.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11018.795404 . ( 0 sec) [ -11014.7165] [GTR parameters ] . ( 0 sec) [ -11014.2861] [Alpha ][ 0.935530] . ( 0 sec) [ -11014.2861] [Topology ] . ( 1 sec) [ -10972.3241] [Topology ] . ( 2 sec) [ -10967.5469] [Topology ] . ( 3 sec) [ -10965.9215] [Topology ] . ( 4 sec) [ -10965.1673] [Topology ] . ( 5 sec) [ -10964.7837] [Topology ] . ( 6 sec) [ -10964.5763] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10964.576298 . ( 13 sec) [ -10964.5099] [GTR parameters ] . ( 13 sec) [ -10963.7218] [Alpha ][ 1.019586] . ( 13 sec) [ -10963.7218] [Topology ] . ( 14 sec) [ -10963.5142] [Topology ] . ( 15 sec) [ -10963.4215] [Topology ] . ( 16 sec) [ -10963.3752] [Topology ] . ( 17 sec) [ -10963.3512] [Topology ] . ( 18 sec) [ -10963.3387] [Topology ] . ( 18 sec) [ -10963.3321] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10963.332126 . ( 25 sec) [ -10963.3319] [GTR parameters ] . ( 25 sec) [ -10963.3219] [Alpha ][ 1.029584] . ( 25 sec) [ -10963.3219] [Topology ] . ( 26 sec) [ -10963.3171] [Topology ] . ( 27 sec) [ -10963.3147] [Topology ] . ( 28 sec) [ -10963.3135] [Topology ] . ( 28 sec) [ -10963.3128] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10963.312816 . ( 35 sec) [ -10963.3128] [GTR parameters ] . ( 35 sec) [ -10963.3127] [Alpha ][ 1.030614] . ( 35 sec) [ -10963.3127] [Topology ] . ( 36 sec) [ -10963.3123] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -11014.7165] [GTR parameters ] . ( 49 sec) [ -11014.2861] [Alpha ][ 0.935530] . ( 49 sec) [ -11014.2447] [ 2544] [depth= 1] . ( 49 sec) [ -11011.8548] [ 2539] [depth= 1] . ( 50 sec) [ -11011.5247] [ 2538] [depth= 1] . ( 51 sec) [ -11011.0193] [ 2539] [depth= 1] . ( 51 sec) [ -11006.3603] [ 2541] [depth= 1] . ( 51 sec) [ -11004.7440] [ 2537] [depth= 1] . ( 51 sec) [ -11001.8465] [ 2536] [depth= 1] . ( 51 sec) [ -11001.3172] [ 2544] [depth= 1] . ( 52 sec) [ -11000.3102] [ 2547] [depth= 1] . ( 52 sec) [ -10999.0709] [ 2544] [depth= 1] . ( 52 sec) [ -10998.7147] [ 2551] [depth= 2] . ( 52 sec) [ -10997.6180] [ 2550] [depth= 1] . ( 52 sec) [ -10996.0019] [ 2544] [depth= 2] . ( 52 sec) [ -10991.6144] [ 2546] [depth= 1] . ( 52 sec) [ -10990.0498] [ 2544] [depth= 1] . ( 52 sec) [ -10969.7566] [Branch lengths ] . ( 53 sec) [ -10969.6992] [GTR parameters ] . ( 53 sec) [ -10969.1724] [Alpha ][ 1.003780] . ( 54 sec) [ -10967.8607] [ 2536] [depth= 1] . ( 54 sec) [ -10967.7681] [ 2541] [depth= 1] . ( 54 sec) [ -10967.0988] [ 2541] [depth= 1] . ( 55 sec) [ -10964.1613] [Branch lengths ] . ( 56 sec) [ -10964.1536] [GTR parameters ] . ( 56 sec) [ -10964.1208] [Alpha ][ 1.021875] . ( 58 sec) [ -10963.8059] [ 2541] [depth= 1] . ( 59 sec) [ -10963.5918] [Branch lengths ] . ( 59 sec) [ -10963.5901] [GTR parameters ] . ( 59 sec) [ -10963.5874] [Alpha ][ 1.027002] . ( 81 sec) [ -10963.5461] [Branch lengths ] . ( 81 sec) [ -10963.5461] [Topology ] . ( 82 sec) [ -10963.3897] [Topology ] . ( 83 sec) [ -10963.3293] [Topology ] . ( 84 sec) [ -10963.3209] [Topology ] . ( 85 sec) [ -10963.3186] [Topology ] . ( 86 sec) [ -10963.3179] [Topology ] . ( 86 sec) [ -10963.3138] [GTR parameters ] . ( 86 sec) [ -10963.3125] [Alpha ][ 1.030547] . ( 86 sec) [ -10963.3125] [Topology ] . ( 87 sec) [ -10963.3121] [Topology ] . ( 87 sec) [ -10963.3120] [GTR parameters ] . ( 87 sec) [ -10963.3120] [Alpha ][ 1.030547] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10963.312327 . Log likelihood obtained after SPR moves : -10963.312046 . Log likelihood of the current tree: -10963.312046. . Printing the most likely tree in file 'data39.phy_phyml_tree.txt'... . Time used 0h1m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo