.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data29.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... . 457 patterns found. (out of a total of 500 sites) . 34 sites without polymorphism (6.80%). . 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=-10897.223759 . ( 0 sec) [ -10895.0531] [GTR parameters ] . ( 0 sec) [ -10892.5292] [Alpha ][ 1.177564] . ( 0 sec) [ -10892.5292] [Topology ] . ( 1 sec) [ -10821.8961] [Topology ] . ( 2 sec) [ -10809.2564] [Topology ] . ( 3 sec) [ -10804.6495] [Topology ] . ( 4 sec) [ -10802.5218] [Topology ] . ( 5 sec) [ -10801.6487] [Topology ] . ( 5 sec) [ -10801.2787] [Topology ] . ( 6 sec) [ -10801.0902] [Topology ] . ( 7 sec) [ -10800.9891] [Topology ] . ( 8 sec) [ -10800.9333] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.902207 . ( 16 sec) [ -10800.8556] [GTR parameters ] . ( 16 sec) [ -10800.7768] [Alpha ][ 1.146085] . ( 16 sec) [ -10800.7768] [Topology ] . ( 17 sec) [ -10800.7500] [Topology ] . ( 18 sec) [ -10800.7373] [Topology ] . ( 18 sec) [ -10800.7301] [Topology ] . ( 19 sec) [ -10800.7259] [Topology ] . ( 20 sec) [ -10800.7235] [Topology ] . ( 21 sec) [ -10800.7221] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.722117 . ( 29 sec) [ -10800.7220] [GTR parameters ] . ( 30 sec) [ -10800.7210] [Alpha ][ 1.142439] . ( 30 sec) [ -10800.7210] [Topology ] . ( 31 sec) [ -10800.7200] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.720028 . ( 38 sec) [ -10800.7200] [GTR parameters ] . ( 38 sec) [ -10800.7200] [Alpha ][ 1.142439] . ( 38 sec) [ -10800.7200] [Topology ] . ( 38 sec) [ -10800.7195] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -10895.0531] [GTR parameters ] . ( 53 sec) [ -10892.5292] [Alpha ][ 1.177564] . ( 53 sec) [ -10890.2018] [ 2589] [depth= 1] . ( 53 sec) [ -10888.2818] [ 2586] [depth= 1] . ( 53 sec) [ -10887.8184] [ 2585] [depth= 1] . ( 53 sec) [ -10882.7191] [ 2586] [depth= 1] . ( 53 sec) [ -10881.9989] [ 2585] [depth= 1] . ( 53 sec) [ -10873.6034] [ 2591] [depth= 1] . ( 53 sec) [ -10869.0209] [ 2585] [depth= 1] . ( 54 sec) [ -10865.5116] [ 2586] [depth= 1] . ( 54 sec) [ -10865.2345] [ 2586] [depth= 1] . ( 54 sec) [ -10865.0865] [ 2588] [depth= 1] . ( 54 sec) [ -10864.0226] [ 2586] [depth= 1] . ( 55 sec) [ -10859.4464] [ 2591] [depth= 4] . ( 55 sec) [ -10858.3842] [ 2592] [depth= 2] . ( 55 sec) [ -10854.5228] [ 2596] [depth= 1] . ( 55 sec) [ -10853.6309] [ 2597] [depth= 1] . ( 55 sec) [ -10852.0951] [ 2596] [depth= 1] . ( 55 sec) [ -10849.3884] [ 2592] [depth= 2] . ( 55 sec) [ -10844.2782] [ 2592] [depth= 1] . ( 55 sec) [ -10838.6564] [ 2584] [depth= 1] . ( 55 sec) [ -10837.5929] [ 2587] [depth= 1] . ( 55 sec) [ -10837.3106] [ 2591] [depth= 1] . ( 56 sec) [ -10837.1915] [ 2594] [depth= 1] . ( 56 sec) [ -10806.9055] [Branch lengths ] . ( 56 sec) [ -10806.8395] [GTR parameters ] . ( 56 sec) [ -10806.7109] [Alpha ][ 1.136825] . ( 57 sec) [ -10806.5491] [ 2599] [depth= 1] . ( 59 sec) [ -10806.4548] [ 2602] [depth= 1] . ( 60 sec) [ -10804.4028] [Branch lengths ] . ( 61 sec) [ -10804.4008] [GTR parameters ] . ( 61 sec) [ -10804.3998] [Alpha ][ 1.133248] . ( 61 sec) [ -10804.3106] [ 2599] [depth= 1] . ( 65 sec) [ -10803.8385] [Branch lengths ] . ( 65 sec) [ -10803.8381] [GTR parameters ] . ( 65 sec) [ -10803.8381] [Alpha ][ 1.133248] . ( 79 sec) [ -10803.5412] [ 2615] [depth= 1] . ( 80 sec) [ -10803.3886] [ 2610] [depth= 1] . ( 82 sec) [ -10802.8064] [ 2608] [depth= 3] . ( 83 sec) [ -10802.4955] [ 2607] [depth= 1] . ( 83 sec) [ -10802.4667] [ 2589] [depth= 1] . ( 86 sec) [ -10802.3605] [ 2601] [depth= 2] . ( 86 sec) [ -10801.3581] [Branch lengths ] . ( 86 sec) [ -10801.3437] [GTR parameters ] . ( 86 sec) [ -10801.3405] [Alpha ][ 1.139483] . ( 102 sec) [ -10801.1752] [ 2594] [depth= 1] . ( 108 sec) [ -10800.8665] [Branch lengths ] . ( 108 sec) [ -10800.8657] [GTR parameters ] . ( 108 sec) [ -10800.8657] [Alpha ][ 1.140622] . ( 108 sec) [ -10800.8657] [Topology ] . ( 109 sec) [ -10800.8311] [Topology ] . ( 110 sec) [ -10800.8184] [Topology ] . ( 111 sec) [ -10800.8127] [Topology ] . ( 111 sec) [ -10800.8101] [Topology ] . ( 112 sec) [ -10800.8088] [Topology ] . ( 113 sec) [ -10800.8083] [Topology ] . ( 113 sec) [ -10800.8082] [GTR parameters ] . ( 113 sec) [ -10800.8082] [Alpha ][ 1.139482] . ( 113 sec) [ -10800.8082] [Topology ] . ( 114 sec) [ -10800.8079] [Topology ] . ( 114 sec) [ -10800.8079] [GTR parameters ] . ( 114 sec) [ -10800.8079] [Alpha ][ 1.139482] . Checking for NNIs, optimizing five branches... . ( 121 sec) [ -10800.7224] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10800.719503 . Log likelihood obtained after SPR moves : -10800.722354 . Log likelihood of the current tree: -10800.719503. . Printing the most likely tree in file 'data29.phy_phyml_tree.txt'... . Time used 0h2m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo