.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data3.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... . 435 patterns found. (out of a total of 500 sites) . 61 sites without polymorphism (12.20%). . 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=-10782.348128 . ( 0 sec) [ -10779.9742] [GTR parameters ] . ( 0 sec) [ -10778.6951] [Alpha ][ 0.893591] . ( 0 sec) [ -10778.6951] [Topology ] . ( 1 sec) [ -10715.7781] [Topology ] . ( 2 sec) [ -10710.3692] [Topology ] . ( 3 sec) [ -10708.8686] [Topology ] . ( 4 sec) [ -10708.2461] [Topology ] . ( 5 sec) [ -10707.9632] [Topology ] . ( 6 sec) [ -10707.8291] [Topology ] . ( 6 sec) [ -10707.7641] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10707.764134 . ( 13 sec) [ -10707.7502] [GTR parameters ] . ( 13 sec) [ -10707.6553] [Alpha ][ 0.919690] . ( 13 sec) [ -10707.6553] [Topology ] . ( 14 sec) [ -10707.6108] [Topology ] . ( 15 sec) [ -10707.5907] [Topology ] . ( 16 sec) [ -10707.5809] [Topology ] . ( 16 sec) [ -10707.5761] [Topology ] . ( 17 sec) [ -10707.5737] [Topology ] . ( 18 sec) [ -10707.5725] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10707.572490 . ( 24 sec) [ -10707.5725] [GTR parameters ] . ( 25 sec) [ -10707.5708] [Alpha ][ 0.923263] . ( 25 sec) [ -10707.5708] [Topology ] . ( 26 sec) [ -10707.5700] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10707.569983 . ( 34 sec) [ -10707.5700] [GTR parameters ] . ( 34 sec) [ -10707.5700] [Alpha ][ 0.923263] . ( 34 sec) [ -10707.5700] [Topology ] . ( 35 sec) [ -10707.5696] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -10779.9742] [GTR parameters ] . ( 49 sec) [ -10778.6951] [Alpha ][ 0.893591] . ( 50 sec) [ -10772.4227] [ 2421] [depth= 1] . ( 50 sec) [ -10769.9177] [ 2426] [depth= 1] . ( 51 sec) [ -10767.6827] [ 2421] [depth= 1] . ( 51 sec) [ -10765.7948] [ 2426] [depth= 1] . ( 51 sec) [ -10762.8481] [ 2421] [depth= 1] . ( 51 sec) [ -10761.5984] [ 2422] [depth= 1] . ( 51 sec) [ -10760.6752] [ 2421] [depth= 1] . ( 51 sec) [ -10759.0631] [ 2424] [depth= 1] . ( 52 sec) [ -10753.5595] [ 2426] [depth= 1] . ( 52 sec) [ -10715.6016] [Branch lengths ] . ( 52 sec) [ -10715.5903] [GTR parameters ] . ( 52 sec) [ -10715.5727] [Alpha ][ 0.905204] . ( 53 sec) [ -10715.1162] [ 2426] [depth= 1] . ( 53 sec) [ -10714.3473] [ 2421] [depth= 1] . ( 54 sec) [ -10714.1892] [ 2421] [depth= 1] . ( 55 sec) [ -10713.4284] [ 2414] [depth= 1] . ( 55 sec) [ -10707.9345] [Branch lengths ] . ( 56 sec) [ -10707.9294] [GTR parameters ] . ( 56 sec) [ -10707.8909] [Alpha ][ 0.922526] . ( 58 sec) [ -10707.5847] [Branch lengths ] . ( 79 sec) [ -10707.5720] [Branch lengths ] . ( 79 sec) [ -10707.5720] [Topology ] . ( 80 sec) [ -10707.5713] [Topology ] . ( 80 sec) [ -10707.5711] [GTR parameters ] . ( 80 sec) [ -10707.5710] [Alpha ][ 0.923448] . ( 80 sec) [ -10707.5710] [Topology ] . ( 81 sec) [ -10707.5708] [Topology ] . ( 81 sec) [ -10707.5708] [GTR parameters ] . ( 81 sec) [ -10707.5708] [Alpha ][ 0.923448] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -10707.5702] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10707.569617 . Log likelihood obtained after SPR moves : -10707.570219 . Log likelihood of the current tree: -10707.569617. . Printing the most likely tree in file 'data3.phy_phyml_tree.txt'... . Time used 0h1m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo