.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data30.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... . 449 patterns found. (out of a total of 500 sites) . 52 sites without polymorphism (10.40%). . 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=-11119.090036 . ( 0 sec) [ -11116.2486] [GTR parameters ] . ( 0 sec) [ -11116.2215] [Alpha ][ 0.984187] . ( 0 sec) [ -11116.2215] [Topology ] . ( 1 sec) [ -11048.5706] [Topology ] . ( 2 sec) [ -11038.8163] [Topology ] . ( 3 sec) [ -11036.5652] [Topology ] . ( 4 sec) [ -11035.6337] [Topology ] . ( 5 sec) [ -11035.1848] [Topology ] . ( 5 sec) [ -11034.9511] [Topology ] . ( 6 sec) [ -11034.8247] [Topology ] . ( 7 sec) [ -11034.7550] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -11034.5574] [Topology ] . Before opt ts/t=1.000000 LK=-11034.557431 . ( 14 sec) [ -11034.4919] [GTR parameters ] . ( 14 sec) [ -11034.4580] [Alpha ][ 1.001854] . ( 14 sec) [ -11034.4580] [Topology ] . ( 15 sec) [ -11034.4100] [Topology ] . ( 16 sec) [ -11034.3880] [Topology ] . ( 17 sec) [ -11034.3763] [Topology ] . ( 18 sec) [ -11034.3700] [Topology ] . ( 19 sec) [ -11034.3664] [Topology ] . ( 20 sec) [ -11034.3645] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11034.364482 . ( 27 sec) [ -11034.3644] [GTR parameters ] . ( 27 sec) [ -11034.3636] [Alpha ][ 1.004582] . ( 27 sec) [ -11034.3636] [Topology ] . ( 27 sec) [ -11034.3623] [Topology ] . ( 28 sec) [ -11034.3616] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11034.361630 . ( 35 sec) [ -11034.3616] [GTR parameters ] . ( 35 sec) [ -11034.3616] [Alpha ][ 1.004582] . ( 35 sec) [ -11034.3616] [Topology ] . ( 36 sec) [ -11034.3612] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -11116.2486] [GTR parameters ] . ( 50 sec) [ -11116.2215] [Alpha ][ 0.984187] . ( 50 sec) [ -11113.9572] [ 2548] [depth= 1] . ( 50 sec) [ -11113.9227] [ 2547] [depth= 1] . ( 50 sec) [ -11113.7576] [ 2548] [depth= 1] . ( 51 sec) [ -11112.2497] [ 2552] [depth= 1] . ( 51 sec) [ -11104.0223] [ 2548] [depth= 1] . ( 51 sec) [ -11100.5631] [ 2549] [depth= 1] . ( 51 sec) [ -11099.9397] [ 2548] [depth= 1] . ( 51 sec) [ -11099.2411] [ 2551] [depth= 1] . ( 51 sec) [ -11092.3177] [ 2553] [depth= 1] . ( 51 sec) [ -11091.7772] [ 2554] [depth= 1] . ( 51 sec) [ -11091.4383] [ 2554] [depth= 1] . ( 52 sec) [ -11091.3842] [ 2559] [depth= 1] . ( 52 sec) [ -11091.3067] [ 2554] [depth= 1] . ( 52 sec) [ -11084.4773] [ 2545] [depth= 2] . ( 52 sec) [ -11083.0147] [ 2548] [depth= 1] . ( 52 sec) [ -11076.7092] [ 2551] [depth= 1] . ( 52 sec) [ -11075.7365] [ 2554] [depth= 1] . ( 53 sec) [ -11073.6798] [ 2550] [depth= 2] . ( 53 sec) [ -11041.3002] [Branch lengths ] . ( 54 sec) [ -11041.2088] [GTR parameters ] . ( 54 sec) [ -11041.2088] [Alpha ][ 0.984187] . ( 54 sec) [ -11041.1949] [ 2549] [depth= 1] . ( 54 sec) [ -11040.9243] [ 2548] [depth= 1] . ( 55 sec) [ -11040.7735] [ 2548] [depth= 1] . ( 56 sec) [ -11039.8719] [ 2548] [depth= 1] . ( 57 sec) [ -11035.4082] [Branch lengths ] . ( 57 sec) [ -11035.3975] [GTR parameters ] . ( 58 sec) [ -11035.3761] [Alpha ][ 0.998295] . ( 58 sec) [ -11035.3427] [ 2547] [depth= 1] . ( 61 sec) [ -11034.4633] [Branch lengths ] . ( 61 sec) [ -11034.4621] [GTR parameters ] . ( 61 sec) [ -11034.4598] [Alpha ][ 1.002912] . ( 83 sec) [ -11034.3779] [Branch lengths ] . ( 84 sec) [ -11034.3779] [Topology ] . ( 85 sec) [ -11034.3684] [Topology ] . ( 86 sec) [ -11034.3650] [Topology ] . ( 87 sec) [ -11034.3633] [Topology ] . ( 88 sec) [ -11034.3624] [Topology ] . ( 88 sec) [ -11034.3623] [GTR parameters ] . ( 88 sec) [ -11034.3619] [Alpha ][ 1.004723] . ( 88 sec) [ -11034.3619] [Topology ] . ( 89 sec) [ -11034.3613] [Topology ] . ( 89 sec) [ -11034.3613] [GTR parameters ] . ( 89 sec) [ -11034.3613] [Alpha ][ 1.004723] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11034.361242 . Log likelihood obtained after SPR moves : -11034.361332 . Log likelihood of the current tree: -11034.361242. . Printing the most likely tree in file 'data30.phy_phyml_tree.txt'... . Time used 0h1m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo