.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2363_38x251_2004.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 : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 244 patterns found. (out of a total of 251 sites) . 24 sites without polymorphism (9.56%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -12114.3207] [Alpha ][ 1.997534] . ( 1 sec) [ -12114.3207] [Topology ] . ( 4 sec) [ -11847.1433] [Topology ] . ( 6 sec) [ -11810.2247] [Topology ] . ( 8 sec) [ -11796.2352] [Topology ] . ( 10 sec) [ -11790.5252] [Topology ] . ( 12 sec) [ -11788.1025] [Topology ] . ( 14 sec) [ -11786.3193] [Topology ] . ( 16 sec) [ -11785.5495] [Topology ] . ( 18 sec) [ -11784.6404] [Topology ] . ( 20 sec) [ -11784.4428] [Topology ] . ( 23 sec) [ -11768.0697] [Alpha ][ 3.989233] . ( 23 sec) [ -11768.0697] [Topology ] . ( 25 sec) [ -11766.7822] [Topology ] . ( 27 sec) [ -11765.7933] [Topology ] . ( 29 sec) [ -11762.8575] [Topology ] . ( 32 sec) [ -11751.5301] [Topology ] . ( 34 sec) [ -11737.3391] [Topology ] . ( 37 sec) [ -11732.6310] [Topology ] . ( 39 sec) [ -11730.8705] [Topology ] . ( 41 sec) [ -11729.8731] [Topology ] . ( 43 sec) [ -11729.3523] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -11728.4647] [Topology ] . ( 72 sec) [ -11726.0651] [Alpha ][ 5.641331] . ( 72 sec) [ -11726.0651] [Topology ] . ( 74 sec) [ -11725.2420] [Topology ] . ( 77 sec) [ -11724.9469] [Topology ] . ( 79 sec) [ -11724.7936] [Topology ] . ( 81 sec) [ -11724.7028] [Topology ] . ( 84 sec) [ -11724.6433] [Topology ] . ( 86 sec) [ -11724.6014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 113 sec) [ -11724.0547] [Topology ] . ( 113 sec) [ -11723.8042] [Alpha ][ 6.378908] . ( 113 sec) [ -11723.8042] [Topology ] . ( 116 sec) [ -11723.5699] [Topology ] . ( 118 sec) [ -11723.5038] [Topology ] . ( 120 sec) [ -11723.4695] [Topology ] . ( 122 sec) [ -11723.4462] [Topology ] . ( 125 sec) [ -11723.4284] [Topology ] . ( 127 sec) [ -11723.4139] [Topology ] . Checking for NNIs, optimizing five branches... . ( 152 sec) [ -11723.4136] [Topology ] . ( 152 sec) [ -11723.3871] [Alpha ][ 6.650675] . ( 153 sec) [ -11723.3871] [Topology ] . ( 155 sec) [ -11723.3677] [Topology ] . ( 157 sec) [ -11723.3473] [Topology ] . ( 159 sec) [ -11723.3235] [Topology ] . ( 162 sec) [ -11723.3043] [Topology ] . ( 164 sec) [ -11723.2885] [Topology ] . ( 166 sec) [ -11723.2756] [Topology ] . Checking for NNIs, optimizing five branches... . ( 192 sec) [ -11723.2744] [Alpha ][ 6.711318] . ( 192 sec) [ -11723.2744] [Topology ] . ( 194 sec) [ -11723.2635] [Topology ] . ( 197 sec) [ -11723.2547] [Topology ] . ( 199 sec) [ -11723.2475] [Topology ] . ( 201 sec) [ -11723.2417] [Topology ] . ( 203 sec) [ -11723.2369] [Topology ] . ( 206 sec) [ -11723.2330] [Topology ] . Checking for NNIs, optimizing five branches... . ( 231 sec) [ -11723.2328] [Alpha ][ 6.735009] . ( 231 sec) [ -11723.2328] [Topology ] . ( 233 sec) [ -11723.2296] [Topology ] . ( 235 sec) [ -11723.2271] [Topology ] . ( 238 sec) [ -11723.2250] [Topology ] . ( 240 sec) [ -11723.2233] [Topology ] . ( 242 sec) [ -11723.2220] [Topology ] . ( 245 sec) [ -11723.2209] [Topology ] . Checking for NNIs, optimizing five branches... . ( 269 sec) [ -11723.2208] [Alpha ][ 6.745605] . ( 269 sec) [ -11723.2208] [Topology ] . ( 272 sec) [ -11723.2199] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 321 sec) [ -12114.3207] [Alpha ][ 1.997534] . ( 322 sec) [ -12110.8932] [ 2680] [depth= 1] . ( 322 sec) [ -12110.4070] [ 2682] [depth= 1] . ( 322 sec) [ -12110.2346] [ 2680] [depth= 1] . ( 323 sec) [ -12100.5882] [ 2676] [depth= 1] . ( 324 sec) [ -12099.5999] [ 2677] [depth= 1] . ( 324 sec) [ -12070.9114] [ 2680] [depth= 2] . ( 324 sec) [ -12069.5901] [ 2680] [depth= 1] . ( 325 sec) [ -12037.4390] [ 2679] [depth= 1] . ( 325 sec) [ -12032.5684] [ 2679] [depth= 1] . ( 326 sec) [ -12029.4027] [ 2678] [depth= 1] . ( 333 sec) [ -12029.3224] [ 2682] [depth= 1] . ( 334 sec) [ -12026.5579] [ 2685] [depth= 1] . ( 334 sec) [ -11996.3150] [ 2682] [depth= 1] . ( 335 sec) [ -11996.3034] [ 2675] [depth= 3] . ( 336 sec) [ -11995.8486] [ 2674] [depth= 1] . ( 337 sec) [ -11994.3122] [ 2674] [depth= 2] . ( 337 sec) [ -11980.3131] [ 2675] [depth= 2] . ( 338 sec) [ -11971.4374] [ 2677] [depth= 4] . ( 339 sec) [ -11958.0486] [ 2677] [depth= 3] . ( 339 sec) [ -11952.8312] [ 2674] [depth= 2] . ( 340 sec) [ -11949.9584] [ 2676] [depth= 1] . ( 340 sec) [ -11939.1935] [ 2678] [depth= 1] . ( 343 sec) [ -11896.9614] [ 2676] [depth= 1] . ( 343 sec) [ -11893.9444] [ 2679] [depth= 1] . ( 343 sec) [ -11890.3046] [ 2682] [depth= 1] . ( 344 sec) [ -11889.1187] [ 2681] [depth= 1] . ( 344 sec) [ -11858.9227] [ 2684] [depth= 1] . ( 345 sec) [ -11853.8631] [ 2681] [depth= 1] . ( 345 sec) [ -11849.8898] [ 2683] [depth= 1] . ( 345 sec) [ -11844.4896] [ 2691] [depth= 1] . ( 346 sec) [ -11837.9036] [ 2691] [depth= 4] . ( 346 sec) [ -11836.1449] [ 2694] [depth= 1] . ( 347 sec) [ -11830.5738] [ 2682] [depth= 3] . ( 347 sec) [ -11828.3091] [ 2677] [depth= 2] . ( 347 sec) [ -11826.3234] [ 2675] [depth= 1] . ( 349 sec) [ -11825.0977] [ 2679] [depth= 3] . ( 350 sec) [ -11820.4917] [ 2682] [depth= 3] . ( 351 sec) [ -11818.6907] [ 2684] [depth= 2] . ( 351 sec) [ -11817.3830] [ 2685] [depth= 1] . ( 352 sec) [ -11815.5880] [ 2684] [depth= 1] . ( 352 sec) [ -11815.0178] [ 2681] [depth= 3] . ( 352 sec) [ -11814.5392] [ 2681] [depth= 3] . ( 354 sec) [ -11811.3536] [ 2685] [depth= 4] . ( 355 sec) [ -11780.1590] [Branch lengths ] . ( 356 sec) [ -11759.9574] [Alpha ][ 3.990621] . ( 359 sec) [ -11736.7077] [ 2679] [depth= 1] . ( 360 sec) [ -11736.2167] [ 2683] [depth= 1] . ( 360 sec) [ -11735.7741] [ 2683] [depth= 1] . ( 367 sec) [ -11735.4868] [ 2685] [depth= 1] . ( 372 sec) [ -11735.1508] [ 2682] [depth= 2] . ( 374 sec) [ -11734.5591] [ 2683] [depth= 2] . ( 374 sec) [ -11734.1263] [ 2687] [depth= 1] . ( 378 sec) [ -11734.1143] [ 2685] [depth= 1] . ( 379 sec) [ -11733.4633] [ 2680] [depth= 1] . ( 382 sec) [ -11731.9379] [ 2676] [depth= 4] . ( 383 sec) [ -11731.1082] [ 2679] [depth= 7] . ( 386 sec) [ -11729.8617] [ 2680] [depth= 1] . ( 387 sec) [ -11727.3337] [ 2669] [depth= 4] . ( 388 sec) [ -11727.1254] [ 2671] [depth= 3] . ( 388 sec) [ -11726.6312] [ 2678] [depth= 1] . ( 394 sec) [ -11726.5293] [ 2679] [depth= 2] . ( 395 sec) [ -11726.4940] [ 2679] [depth= 1] . ( 395 sec) [ -11716.7434] [Branch lengths ] . ( 396 sec) [ -11714.9961] [Alpha ][ 5.388255] . ( 399 sec) [ -11714.9716] [ 2677] [depth= 1] . ( 421 sec) [ -11714.9531] [ 2674] [depth= 1] . ( 423 sec) [ -11714.7916] [ 2675] [depth= 1] . ( 426 sec) [ -11714.7552] [ 2680] [depth= 1] . ( 429 sec) [ -11714.3590] [ 2680] [depth= 1] . ( 430 sec) [ -11714.3341] [ 2682] [depth= 1] . ( 431 sec) [ -11713.9644] [ 2681] [depth= 2] . ( 439 sec) [ -11713.5023] [ 2681] [depth= 2] . ( 440 sec) [ -11710.9663] [Branch lengths ] . ( 441 sec) [ -11710.7946] [Alpha ][ 5.948914] . ( 444 sec) [ -11710.6128] [ 2682] [depth= 1] . ( 445 sec) [ -11710.5781] [ 2675] [depth= 1] . ( 494 sec) [ -11710.5592] [ 2680] [depth= 2] . ( 495 sec) [ -11709.1816] [Branch lengths ] . ( 495 sec) [ -11709.1557] [Alpha ][ 6.191678] . ( 553 sec) [ -11708.6791] [Branch lengths ] . ( 553 sec) [ -11708.6791] [Topology ] . ( 556 sec) [ -11708.5810] [Topology ] . ( 558 sec) [ -11708.5284] [Topology ] . ( 560 sec) [ -11708.5028] [Topology ] . ( 563 sec) [ -11708.4928] [Topology ] . ( 565 sec) [ -11708.4890] [Topology ] . ( 567 sec) [ -11708.4871] [Topology ] . ( 568 sec) [ -11708.4800] [Alpha ][ 6.322708] . ( 568 sec) [ -11708.4800] [Topology ] . ( 570 sec) [ -11708.4777] [Topology ] . ( 573 sec) [ -11708.4767] [Topology ] . ( 575 sec) [ -11708.4761] [Topology ] . ( 575 sec) [ -11708.4757] [Alpha ][ 6.353911] . ( 576 sec) [ -11708.4757] [Topology ] . ( 578 sec) [ -11708.4752] [Topology ] . ( 578 sec) [ -11708.4752] [Alpha ][ 6.360265] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11723.219946 . Log likelihood obtained after SPR moves : -11708.475193 . Log likelihood of the current tree: -11708.475193. . Printing the most likely tree in file 'proteic_M2363_38x251_2004.phy_phyml_tree.txt'... . Time used 0h10m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 604.33user 0.00system 10:05.37elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps