.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1385_11x530_2003.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 312 patterns found. (out of a total of 530 sites) . 226 sites without polymorphism (42.64%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6309.2720] [Alpha ][ 0.500960] . ( 1 sec) [ -6269.0280] [ 904] [depth= 2] . ( 1 sec) [ -6164.5298] [ 885] [depth= 3] . ( 1 sec) [ -6100.3036] [ 879] [depth= 2] . ( 1 sec) [ -6063.0644] [ 875] [depth= 1] . ( 1 sec) [ -5953.6908] [ 842] [depth= 1] . ( 2 sec) [ -5947.7246] [ 841] [depth= 1] . ( 2 sec) [ -5851.5293] [ 839] [depth= 1] . ( 2 sec) [ -5845.9171] [ 841] [depth= 1] . ( 2 sec) [ -5792.8817] [ 843] [depth= 3] . ( 2 sec) [ -5786.9358] [ 844] [depth= 1] . ( 3 sec) [ -5717.8977] [ 840] [depth= 2] . ( 3 sec) [ -5673.1344] [ 824] [depth= 1] . ( 3 sec) [ -5661.6461] [ 822] [depth= 2] . ( 3 sec) [ -5644.8979] [ 813] [depth= 3] . ( 4 sec) [ -5629.9087] [ 813] [depth= 2] . ( 4 sec) [ -5625.9418] [ 809] [depth= 3] . ( 4 sec) [ -5624.6155] [ 809] [depth= 1] . ( 5 sec) [ -5619.1506] [Branch lengths ] . ( 5 sec) [ -5617.2576] [Alpha ][ 0.605259] . ( 6 sec) [ -5616.7592] [ 809] [depth= 1] . ( 9 sec) [ -5615.7860] [ 811] [depth= 2] . ( 10 sec) [ -5611.8594] [ 811] [depth= 1] . ( 18 sec) [ -5609.8655] [Branch lengths ] . ( 18 sec) [ -5609.8520] [Alpha ][ 0.615362] . ( 33 sec) [ -5609.8186] [Branch lengths ] . ( 33 sec) [ -5609.8186] [Topology ] . ( 34 sec) [ -5609.8178] [Topology ] . ( 34 sec) [ -5609.8177] [Alpha ][ 0.616091] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5609.4771] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5609.477094. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6248.2898] [Alpha ][ 0.500960] . ( 1 sec) [ -6036.9677] [ 915] [depth= 2] . ( 1 sec) [ -5964.3702] [ 906] [depth= 3] . ( 1 sec) [ -5941.0827] [ 901] [depth= 2] . ( 1 sec) [ -5932.0395] [ 896] [depth= 1] . ( 1 sec) [ -5911.0042] [ 884] [depth= 4] . ( 2 sec) [ -5882.6458] [ 868] [depth= 1] . ( 2 sec) [ -5834.8588] [ 868] [depth= 2] . ( 2 sec) [ -5816.9679] [ 852] [depth= 1] . ( 2 sec) [ -5795.0120] [ 840] [depth= 3] . ( 2 sec) [ -5689.7319] [ 815] [depth= 1] . ( 2 sec) [ -5683.8158] [ 813] [depth= 1] . ( 3 sec) [ -5661.5786] [ 810] [depth= 2] . ( 3 sec) [ -5649.9505] [ 813] [depth= 1] . ( 3 sec) [ -5636.5265] [ 808] [depth= 3] . ( 6 sec) [ -5615.3678] [Branch lengths ] . ( 6 sec) [ -5612.9953] [Alpha ][ 0.619474] . ( 16 sec) [ -5612.4951] [Branch lengths ] . ( 16 sec) [ -5612.4951] [Topology ] . ( 17 sec) [ -5612.4800] [Topology ] . ( 18 sec) [ -5612.4759] [Topology ] . ( 18 sec) [ -5612.4743] [Topology ] . ( 19 sec) [ -5612.4736] [Topology ] . ( 19 sec) [ -5612.4683] [Alpha ][ 0.625950] . ( 19 sec) [ -5612.4683] [Topology ] . ( 19 sec) [ -5612.4676] [Topology ] . ( 19 sec) [ -5612.4676] [Alpha ][ 0.625950] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5612.467613. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6249.2012] [Alpha ][ 0.500960] . ( 0 sec) [ -6175.8013] [ 894] [depth= 2] . ( 0 sec) [ -5941.7081] [ 879] [depth= 3] . ( 0 sec) [ -5919.4746] [ 879] [depth= 1] . ( 1 sec) [ -5847.5101] [ 872] [depth= 1] . ( 1 sec) [ -5834.2374] [ 869] [depth= 1] . ( 1 sec) [ -5803.7661] [ 861] [depth= 2] . ( 1 sec) [ -5698.7604] [ 831] [depth= 1] . ( 1 sec) [ -5692.5298] [ 836] [depth= 1] . ( 1 sec) [ -5692.4901] [ 837] [depth= 1] . ( 1 sec) [ -5680.3279] [ 837] [depth= 3] . ( 2 sec) [ -5679.7786] [ 836] [depth= 1] . ( 2 sec) [ -5677.4170] [ 835] [depth= 2] . ( 2 sec) [ -5676.0463] [ 833] [depth= 1] . ( 3 sec) [ -5629.6629] [ 814] [depth= 2] . ( 3 sec) [ -5628.7658] [ 812] [depth= 3] . ( 4 sec) [ -5627.2135] [ 811] [depth= 1] . ( 5 sec) [ -5627.1536] [ 813] [depth= 1] . ( 5 sec) [ -5621.8487] [Branch lengths ] . ( 5 sec) [ -5619.9596] [Alpha ][ 0.603091] . ( 8 sec) [ -5619.8074] [ 809] [depth= 2] . ( 9 sec) [ -5617.9767] [ 811] [depth= 1] . ( 12 sec) [ -5617.2376] [ 812] [depth= 2] . ( 13 sec) [ -5617.1963] [ 817] [depth= 1] . ( 16 sec) [ -5615.7305] [Branch lengths ] . ( 16 sec) [ -5615.7286] [Alpha ][ 0.599298] . ( 19 sec) [ -5612.3454] [ 810] [depth= 1] . ( 22 sec) [ -5611.8110] [ 812] [depth= 1] . ( 28 sec) [ -5609.5992] [Branch lengths ] . ( 28 sec) [ -5609.5599] [Alpha ][ 0.615797] . ( 43 sec) [ -5609.4697] [Branch lengths ] . ( 43 sec) [ -5609.4697] [Topology ] . ( 44 sec) [ -5609.4671] [Topology ] . ( 44 sec) [ -5609.4667] [Topology ] . ( 44 sec) [ -5609.4662] [Alpha ][ 0.613722] . ( 44 sec) [ -5609.4662] [Topology ] . ( 45 sec) [ -5609.4659] [Topology ] . ( 45 sec) [ -5609.4659] [Alpha ][ 0.613722] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5609.465937. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6198.0647] [Alpha ][ 0.500960] . ( 1 sec) [ -6141.3701] [ 911] [depth= 4] . ( 1 sec) [ -5938.4775] [ 895] [depth= 4] . ( 1 sec) [ -5886.9029] [ 892] [depth= 1] . ( 1 sec) [ -5850.5789] [ 877] [depth= 1] . ( 1 sec) [ -5839.1460] [ 868] [depth= 2] . ( 2 sec) [ -5834.5335] [ 865] [depth= 1] . ( 2 sec) [ -5810.9684] [ 864] [depth= 2] . ( 2 sec) [ -5792.9422] [ 854] [depth= 2] . ( 2 sec) [ -5773.7288] [ 850] [depth= 1] . ( 2 sec) [ -5762.6754] [ 844] [depth= 2] . ( 3 sec) [ -5753.0829] [ 843] [depth= 1] . ( 3 sec) [ -5735.4407] [ 838] [depth= 2] . ( 4 sec) [ -5733.0315] [ 838] [depth= 1] . ( 4 sec) [ -5635.1226] [ 811] [depth= 1] . ( 7 sec) [ -5616.9175] [Branch lengths ] . ( 7 sec) [ -5615.0101] [Alpha ][ 0.606426] . ( 11 sec) [ -5612.7440] [ 811] [depth= 1] . ( 21 sec) [ -5609.9258] [Branch lengths ] . ( 21 sec) [ -5609.9199] [Alpha ][ 0.613070] . ( 36 sec) [ -5609.8241] [Branch lengths ] . ( 36 sec) [ -5609.8241] [Topology ] . ( 37 sec) [ -5609.8204] [Topology ] . ( 37 sec) [ -5609.8195] [Topology ] . ( 37 sec) [ -5609.8184] [Alpha ][ 0.615886] . ( 37 sec) [ -5609.8184] [Topology ] . ( 38 sec) [ -5609.8180] [Topology ] . ( 38 sec) [ -5609.8180] [Alpha ][ 0.615886] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -5609.4781] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5609.478125. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6176.9800] [Alpha ][ 0.500960] . ( 0 sec) [ -6042.8559] [ 898] [depth= 5] . ( 0 sec) [ -5946.8489] [ 879] [depth= 5] . ( 0 sec) [ -5918.4936] [ 879] [depth= 1] . ( 0 sec) [ -5888.1197] [ 874] [depth= 1] . ( 1 sec) [ -5857.7999] [ 857] [depth= 2] . ( 1 sec) [ -5846.6472] [ 858] [depth= 1] . ( 1 sec) [ -5837.1425] [ 854] [depth= 1] . ( 1 sec) [ -5730.2071] [ 814] [depth= 1] . ( 2 sec) [ -5650.2515] [ 809] [depth= 3] . ( 2 sec) [ -5646.8422] [ 809] [depth= 1] . ( 2 sec) [ -5645.3305] [ 809] [depth= 1] . ( 3 sec) [ -5640.5584] [ 811] [depth= 2] . ( 3 sec) [ -5634.1871] [ 811] [depth= 1] . ( 4 sec) [ -5628.4390] [ 810] [depth= 2] . ( 4 sec) [ -5613.0869] [Branch lengths ] . ( 4 sec) [ -5611.1631] [Alpha ][ 0.605504] . ( 11 sec) [ -5610.3449] [ 812] [depth= 1] . ( 14 sec) [ -5609.4864] [Branch lengths ] . ( 14 sec) [ -5609.4783] [Alpha ][ 0.613323] . ( 29 sec) [ -5609.4663] [Branch lengths ] . ( 29 sec) [ -5609.4663] [Topology ] . ( 30 sec) [ -5609.4659] [Topology ] . ( 30 sec) [ -5609.4659] [Alpha ][ 0.613323] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5609.465927. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -5642.0556] [Alpha ][ 0.522309] . ( 0 sec) [ -5642.0556] [Topology ] . ( 1 sec) [ -5615.4964] [Topology ] . ( 1 sec) [ -5612.0959] [Topology ] . ( 2 sec) [ -5611.4656] [Topology ] . ( 3 sec) [ -5611.3011] [Topology ] . ( 3 sec) [ -5611.2430] [Topology ] . ( 4 sec) [ -5611.2203] [Topology ] . ( 4 sec) [ -5611.2109] [Topology ] . ( 5 sec) [ -5611.2070] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -5610.8025] [Topology ] . ( 9 sec) [ -5609.5704] [Alpha ][ 0.608297] . ( 9 sec) [ -5609.5704] [Topology ] . ( 9 sec) [ -5609.4986] [Topology ] . ( 10 sec) [ -5609.4808] [Topology ] . ( 11 sec) [ -5609.4741] [Topology ] . ( 11 sec) [ -5609.4715] [Topology ] . ( 12 sec) [ -5609.4704] [Topology ] . ( 12 sec) [ -5609.4699] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -5609.4666] [Alpha ][ 0.613307] . ( 16 sec) [ -5609.4666] [Topology ] . ( 17 sec) [ -5609.4661] [Topology ] . Checking for NNIs, optimizing five branches... . ( 21 sec) [ -5609.4661] [Alpha ][ 0.613307] . ( 21 sec) [ -5609.4661] [Topology ] . ( 21 sec) [ -5609.4659] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 29 sec) [ -5642.0556] [Alpha ][ 0.522309] . ( 30 sec) [ -5637.6028] [ 810] [depth= 1] . ( 30 sec) [ -5634.9800] [ 810] [depth= 2] . ( 31 sec) [ -5629.0229] [ 810] [depth= 2] . ( 31 sec) [ -5626.5004] [ 808] [depth= 2] . ( 31 sec) [ -5622.7591] [ 810] [depth= 1] . ( 31 sec) [ -5619.9301] [ 811] [depth= 1] . ( 38 sec) [ -5611.6151] [Branch lengths ] . ( 39 sec) [ -5610.5402] [Alpha ][ 0.603118] . ( 54 sec) [ -5609.9095] [Branch lengths ] . ( 54 sec) [ -5609.9095] [Topology ] . ( 54 sec) [ -5609.8621] [Topology ] . ( 55 sec) [ -5609.8492] [Topology ] . ( 55 sec) [ -5609.8441] [Topology ] . ( 56 sec) [ -5609.8421] [Topology ] . ( 56 sec) [ -5609.8412] [Topology ] . ( 57 sec) [ -5609.8201] [Alpha ][ 0.615160] . ( 57 sec) [ -5609.8201] [Topology ] . ( 57 sec) [ -5609.8187] [Topology ] . ( 58 sec) [ -5609.8181] [Topology ] . ( 58 sec) [ -5609.8181] [Alpha ][ 0.615892] . ( 58 sec) [ -5609.8181] [Topology ] . ( 58 sec) [ -5609.8178] [Topology ] . ( 58 sec) [ -5609.8178] [Alpha ][ 0.615892] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -5609.4780] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5609.465950 . Log likelihood obtained after SPR moves : -5609.477962 . Log likelihood of the current tree: -5609.465950. . Printing the most likely tree in file 'proteic_M1385_11x530_2003.phy_phyml_tree.txt'... . Best log likelihood : -5609.465927 . Time used 0h1m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 259.68user 0.00system 4:22.61elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps