.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1991_32x129_2004.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : LG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : no . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 9 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 113 patterns found. (out of a total of 129 sites) . 25 sites without polymorphism (19.38%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2529.3361] [ 429] [depth= 1] . ( 0 sec) [ -2528.1374] [ 429] [depth= 1] . ( 0 sec) [ -2527.6450] [ 429] [depth= 1] . ( 0 sec) [ -2515.8855] [ 427] [depth= 3] . ( 0 sec) [ -2515.6424] [ 427] [depth= 1] . ( 1 sec) [ -2510.8637] [ 428] [depth= 1] . ( 1 sec) [ -2507.9954] [ 427] [depth= 1] . ( 5 sec) [ -2502.0825] [ 424] [depth= 1] . ( 5 sec) [ -2499.8640] [ 423] [depth= 1] . ( 5 sec) [ -2482.8561] [ 427] [depth= 2] . ( 6 sec) [ -2471.1565] [ 431] [depth= 2] . ( 6 sec) [ -2456.6148] [ 427] [depth= 2] . ( 6 sec) [ -2456.0909] [ 427] [depth= 1] . ( 6 sec) [ -2455.0388] [ 427] [depth= 1] . ( 7 sec) [ -2448.2297] [ 427] [depth= 1] . ( 7 sec) [ -2423.7775] [ 423] [depth= 1] . ( 7 sec) [ -2421.2434] [ 423] [depth= 1] . ( 7 sec) [ -2417.8762] [ 425] [depth= 4] . ( 8 sec) [ -2416.4974] [ 428] [depth= 6] . ( 9 sec) [ -2416.3761] [ 425] [depth= 4] . ( 10 sec) [ -2415.0963] [ 427] [depth= 1] . ( 12 sec) [ -2413.8254] [ 427] [depth= 1] . ( 13 sec) [ -2412.7306] [ 425] [depth= 1] . ( 16 sec) [ -2409.2557] [ 424] [depth= 1] . ( 16 sec) [ -2408.9177] [ 425] [depth= 1] . ( 17 sec) [ -2408.7953] [ 426] [depth= 1] . ( 24 sec) [ -2408.6497] [ 425] [depth= 1] . ( 24 sec) [ -2408.6149] [ 426] [depth= 1] . ( 24 sec) [ -2408.4496] [ 425] [depth= 1] . ( 24 sec) [ -2405.5627] [ 425] [depth= 3] . ( 29 sec) [ -2405.2582] [ 425] [depth= 1] . ( 30 sec) [ -2404.9508] [ 425] [depth= 1] . ( 31 sec) [ -2400.3722] [Branch lengths ] . ( 33 sec) [ -2400.3605] [ 425] [depth= 1] . ( 51 sec) [ -2400.2919] [ 427] [depth= 5] . ( 57 sec) [ -2400.0781] [ 426] [depth= 1] . ( 80 sec) [ -2399.8007] [Branch lengths ] . ( 80 sec) [ -2399.8007] [Topology ] . ( 81 sec) [ -2399.7575] [Topology ] . ( 82 sec) [ -2399.7291] [Topology ] . ( 83 sec) [ -2399.7060] [Topology ] . ( 84 sec) [ -2399.6865] [Topology ] . ( 85 sec) [ -2399.6693] [Topology ] . ( 86 sec) [ -2399.6540] [Topology ] . ( 86 sec) [ -2399.6540] [Topology ] . ( 87 sec) [ -2399.6403] [Topology ] . ( 88 sec) [ -2399.6278] [Topology ] . ( 89 sec) [ -2399.6165] [Topology ] . ( 90 sec) [ -2399.6062] [Topology ] . ( 91 sec) [ -2399.5968] [Topology ] . ( 91 sec) [ -2399.5882] [Topology ] . ( 92 sec) [ -2399.5882] [Topology ] . ( 92 sec) [ -2399.5802] [Topology ] . ( 93 sec) [ -2399.5728] [Topology ] . ( 94 sec) [ -2399.5660] [Topology ] . ( 95 sec) [ -2399.5597] [Topology ] . ( 96 sec) [ -2399.5538] [Topology ] . ( 97 sec) [ -2399.5484] [Topology ] . ( 97 sec) [ -2399.5484] [Topology ] . ( 98 sec) [ -2399.5433] [Topology ] . ( 99 sec) [ -2399.5400] [Topology ] . ( 100 sec) [ -2399.5387] [Topology ] . ( 101 sec) [ -2399.5383] [Topology ] . ( 101 sec) [ -2399.5383] [Topology ] . ( 102 sec) [ -2399.5382] [Topology ] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -2399.5252] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2399.525226. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 38 8.823896 0.798000 0.045586 13 -1.000000 0.000000 0.000000 42 12.162802 0.896000 0.068810 45 27.271838 0.953000 0.122065 36 4.708418 0.520000 0.066169 31 1.592470 0.766000 0.166304 65 328.060196 1.000000 2.126832 14 0.303506 0.075000 0.042912 2 0.768596 0.664000 0.014300 1 1.021543 0.098000 0.054640 85 8.327543 0.864000 0.052943 40 1.682848 0.318000 0.010274 4 23.954907 0.955000 0.145101 3 -1.000000 0.000000 0.020935 25 -1.000000 0.000000 0.019772 53 9.799105 0.815000 0.036896 17 1.053389 0.670000 0.015596 7 -1.000000 0.000000 0.000001 30 1.234852 0.202000 0.010783 58 13.590770 0.880000 0.028978 77 4.133460 0.757000 0.015527 5 0.026168 0.000000 0.067732 22 5.477110 0.815000 0.033230 83 34.264959 0.966000 0.102765 98 43.668647 0.987000 0.088915 30 -1.000000 0.000000 0.000010 49 6.037886 0.773000 0.019305 62 5.191161 0.754000 0.014575 20 -1.000000 0.000000 0.000001 . Printing the most likely tree in file 'proteic_M1991_32x129_2004.phy_phyml_tree.txt'... . Time used 4h5m21s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo