.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data90.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... . 399 patterns found. (out of a total of 500 sites) . 100 sites without polymorphism (20.00%). . 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=-7804.366693 . ( 1 sec) [ -7802.1644] [GTR parameters ] . ( 1 sec) [ -7801.9691] [Alpha ][ 0.948006] . ( 1 sec) [ -7801.9691] [Topology ] . ( 1 sec) [ -7762.6758] [Topology ] . ( 2 sec) [ -7752.3946] [Topology ] . ( 3 sec) [ -7747.7755] [Topology ] . ( 4 sec) [ -7744.2828] [Topology ] . ( 5 sec) [ -7742.8247] [Topology ] . ( 6 sec) [ -7742.5889] [Topology ] . ( 7 sec) [ -7742.5291] [Topology ] . ( 8 sec) [ -7742.5065] [Topology ] . ( 8 sec) [ -7742.4959] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -7742.4158] [Topology ] . Before opt ts/t=1.000000 LK=-7742.415787 . ( 17 sec) [ -7742.4033] [GTR parameters ] . ( 17 sec) [ -7742.1531] [Alpha ][ 1.005038] . ( 17 sec) [ -7742.1531] [Topology ] . ( 18 sec) [ -7742.1429] [Topology ] . ( 19 sec) [ -7742.1399] [Topology ] . ( 20 sec) [ -7742.1387] [Topology ] . ( 21 sec) [ -7742.1382] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7742.138223 . ( 30 sec) [ -7742.1382] [GTR parameters ] . ( 30 sec) [ -7742.1378] [Alpha ][ 1.007282] . ( 30 sec) [ -7742.1378] [Topology ] . ( 31 sec) [ -7742.1375] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 47 sec) [ -7802.1644] [GTR parameters ] . ( 47 sec) [ -7801.9691] [Alpha ][ 0.948006] . ( 48 sec) [ -7801.9550] [ 1577] [depth= 1] . ( 48 sec) [ -7801.9414] [ 1577] [depth= 1] . ( 48 sec) [ -7801.6532] [ 1577] [depth= 1] . ( 48 sec) [ -7797.9590] [ 1575] [depth= 1] . ( 49 sec) [ -7791.7923] [ 1574] [depth= 1] . ( 49 sec) [ -7789.4085] [ 1576] [depth= 2] . ( 49 sec) [ -7788.2794] [ 1573] [depth= 1] . ( 49 sec) [ -7786.3456] [ 1574] [depth= 1] . ( 49 sec) [ -7785.3166] [ 1573] [depth= 1] . ( 49 sec) [ -7784.6914] [ 1575] [depth= 1] . ( 49 sec) [ -7784.6573] [ 1576] [depth= 1] . ( 50 sec) [ -7782.7528] [ 1575] [depth= 1] . ( 51 sec) [ -7782.4295] [ 1576] [depth= 1] . ( 51 sec) [ -7782.4002] [ 1576] [depth= 1] . ( 51 sec) [ -7780.0786] [ 1574] [depth= 2] . ( 51 sec) [ -7768.9048] [ 1575] [depth= 4] . ( 52 sec) [ -7766.0780] [ 1577] [depth= 2] . ( 52 sec) [ -7765.5159] [ 1579] [depth= 1] . ( 52 sec) [ -7765.0402] [ 1580] [depth= 2] . ( 52 sec) [ -7764.4642] [ 1578] [depth= 1] . ( 53 sec) [ -7763.9865] [ 1580] [depth= 1] . ( 53 sec) [ -7763.7058] [ 1573] [depth= 1] . ( 54 sec) [ -7743.6835] [Branch lengths ] . ( 55 sec) [ -7743.6712] [GTR parameters ] . ( 55 sec) [ -7743.5090] [Alpha ][ 0.993719] . ( 55 sec) [ -7743.3733] [ 1573] [depth= 1] . ( 57 sec) [ -7743.3536] [ 1572] [depth= 1] . ( 59 sec) [ -7743.2672] [ 1573] [depth= 1] . ( 60 sec) [ -7743.2511] [ 1578] [depth= 1] . ( 62 sec) [ -7743.0770] [ 1580] [depth= 1] . ( 62 sec) [ -7742.3507] [Branch lengths ] . ( 63 sec) [ -7742.3495] [GTR parameters ] . ( 63 sec) [ -7742.3463] [Alpha ][ 1.000447] . ( 69 sec) [ -7742.2706] [Branch lengths ] . ( 100 sec) [ -7742.2601] [Branch lengths ] . ( 100 sec) [ -7742.2601] [Topology ] . ( 102 sec) [ -7742.2591] [Topology ] . ( 102 sec) [ -7742.2590] [GTR parameters ] . ( 102 sec) [ -7742.2585] [Alpha ][ 1.003264] . ( 102 sec) [ -7742.2585] [Topology ] . ( 103 sec) [ -7742.2580] [Topology ] . ( 104 sec) [ -7742.2580] [GTR parameters ] . ( 104 sec) [ -7742.2580] [Alpha ][ 1.003264] . Checking for NNIs, optimizing five branches... . ( 112 sec) [ -7742.2576] [Topology ] . Checking for NNIs, optimizing five branches... . ( 118 sec) [ -7742.2572] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7742.137484 . Log likelihood obtained after SPR moves : -7742.257181 . Log likelihood of the current tree: -7742.137484. . Printing the most likely tree in file 'data90.phy_phyml_tree.txt'... . Time used 0h2m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo