.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data45.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... . 439 patterns found. (out of a total of 500 sites) . 55 sites without polymorphism (11.00%). . 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=-10249.134706 . ( 1 sec) [ -10245.1148] [GTR parameters ] . ( 1 sec) [ -10243.8466] [Alpha ][ 0.889997] . ( 1 sec) [ -10243.8466] [Topology ] . ( 2 sec) [ -10164.4022] [Topology ] . ( 3 sec) [ -10138.0065] [Topology ] . ( 3 sec) [ -10131.1905] [Topology ] . ( 4 sec) [ -10129.1012] [Topology ] . ( 5 sec) [ -10128.1641] [Topology ] . ( 6 sec) [ -10127.6945] [Topology ] . ( 7 sec) [ -10127.4437] [Topology ] . ( 7 sec) [ -10127.3062] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10127.306184 . ( 14 sec) [ -10127.0631] [GTR parameters ] . ( 14 sec) [ -10126.8625] [Alpha ][ 0.929574] . ( 14 sec) [ -10126.8625] [Topology ] . ( 15 sec) [ -10126.7541] [Topology ] . ( 16 sec) [ -10126.6997] [Topology ] . ( 17 sec) [ -10126.6700] [Topology ] . ( 17 sec) [ -10126.6535] [Topology ] . ( 18 sec) [ -10126.6444] [Topology ] . ( 19 sec) [ -10126.6392] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10126.639199 . ( 25 sec) [ -10126.6387] [GTR parameters ] . ( 25 sec) [ -10126.6362] [Alpha ][ 0.934120] . ( 25 sec) [ -10126.6362] [Topology ] . ( 26 sec) [ -10126.6329] [Topology ] . ( 27 sec) [ -10126.6311] [Topology ] . ( 28 sec) [ -10126.6301] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10126.630135 . ( 34 sec) [ -10126.6301] [GTR parameters ] . ( 34 sec) [ -10126.6301] [Alpha ][ 0.934120] . ( 34 sec) [ -10126.6301] [Topology ] . ( 35 sec) [ -10126.6295] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -10245.1148] [GTR parameters ] . ( 52 sec) [ -10243.8466] [Alpha ][ 0.889997] . ( 52 sec) [ -10238.6405] [ 2364] [depth= 1] . ( 53 sec) [ -10231.1171] [ 2361] [depth= 2] . ( 53 sec) [ -10217.1031] [ 2351] [depth= 1] . ( 53 sec) [ -10208.8573] [ 2363] [depth= 1] . ( 53 sec) [ -10208.4418] [ 2365] [depth= 1] . ( 54 sec) [ -10208.4284] [ 2364] [depth= 1] . ( 54 sec) [ -10207.8106] [ 2369] [depth= 1] . ( 54 sec) [ -10201.9318] [ 2364] [depth= 1] . ( 54 sec) [ -10195.7216] [ 2363] [depth= 1] . ( 55 sec) [ -10187.8812] [ 2364] [depth= 1] . ( 55 sec) [ -10185.9883] [ 2369] [depth= 1] . ( 55 sec) [ -10185.3439] [ 2370] [depth= 1] . ( 55 sec) [ -10183.7502] [ 2373] [depth= 2] . ( 55 sec) [ -10178.9131] [ 2366] [depth= 3] . ( 56 sec) [ -10173.1634] [ 2372] [depth= 1] . ( 56 sec) [ -10172.3758] [ 2373] [depth= 1] . ( 56 sec) [ -10171.6514] [ 2372] [depth= 1] . ( 56 sec) [ -10169.8675] [ 2373] [depth= 1] . ( 56 sec) [ -10169.1876] [ 2377] [depth= 1] . ( 56 sec) [ -10168.4663] [ 2380] [depth= 1] . ( 56 sec) [ -10146.7781] [Branch lengths ] . ( 57 sec) [ -10146.5599] [GTR parameters ] . ( 57 sec) [ -10146.3890] [Alpha ][ 0.926299] . ( 57 sec) [ -10141.9730] [ 2370] [depth= 1] . ( 58 sec) [ -10141.9341] [ 2371] [depth= 1] . ( 58 sec) [ -10141.9009] [ 2370] [depth= 1] . ( 59 sec) [ -10141.0617] [ 2365] [depth= 1] . ( 59 sec) [ -10140.4559] [ 2366] [depth= 1] . ( 59 sec) [ -10137.6579] [ 2371] [depth= 1] . ( 59 sec) [ -10137.5992] [ 2371] [depth= 1] . ( 60 sec) [ -10136.2718] [ 2363] [depth= 1] . ( 60 sec) [ -10135.3541] [ 2365] [depth= 1] . ( 61 sec) [ -10128.2168] [Branch lengths ] . ( 61 sec) [ -10128.1278] [GTR parameters ] . ( 61 sec) [ -10128.1261] [Alpha ][ 0.930112] . ( 65 sec) [ -10127.6984] [Branch lengths ] . ( 72 sec) [ -10127.6260] [ 2350] [depth= 1] . ( 81 sec) [ -10127.3138] [ 2346] [depth= 1] . ( 86 sec) [ -10126.8579] [Branch lengths ] . ( 86 sec) [ -10126.8555] [GTR parameters ] . ( 86 sec) [ -10126.8528] [Alpha ][ 0.934841] . ( 86 sec) [ -10126.8528] [Topology ] . ( 87 sec) [ -10126.7864] [Topology ] . ( 88 sec) [ -10126.7550] [Topology ] . ( 89 sec) [ -10126.7457] [Topology ] . ( 90 sec) [ -10126.7415] [Topology ] . ( 91 sec) [ -10126.7395] [Topology ] . ( 91 sec) [ -10126.7385] [Topology ] . ( 92 sec) [ -10126.7379] [Topology ] . ( 92 sec) [ -10126.7377] [GTR parameters ] . ( 92 sec) [ -10126.7376] [Alpha ][ 0.935776] . ( 92 sec) [ -10126.7376] [Topology ] . ( 93 sec) [ -10126.7373] [Topology ] . ( 93 sec) [ -10126.7373] [GTR parameters ] . ( 93 sec) [ -10126.7373] [Alpha ][ 0.935776] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -10126.6375] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10126.629534 . Log likelihood obtained after SPR moves : -10126.637464 . Log likelihood of the current tree: -10126.629534. . Printing the most likely tree in file 'data45.phy_phyml_tree.txt'... . Time used 0h1m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo