.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1508_22x431_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... . 172 patterns found. (out of a total of 431 sites) . 298 sites without polymorphism (69.14%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3771.2520] [Alpha ][ 0.500960] . ( 1 sec) [ -3673.1009] [ 381] [depth= 8] . ( 1 sec) [ -3652.0720] [ 380] [depth= 2] . ( 1 sec) [ -3647.8742] [ 378] [depth= 1] . ( 1 sec) [ -3618.4932] [ 376] [depth= 3] . ( 1 sec) [ -3601.3215] [ 374] [depth= 3] . ( 1 sec) [ -3596.9203] [ 369] [depth= 5] . ( 1 sec) [ -3581.3621] [ 367] [depth= 2] . ( 2 sec) [ -3572.3692] [ 366] [depth= 1] . ( 2 sec) [ -3568.9172] [ 367] [depth= 1] . ( 2 sec) [ -3513.9995] [ 369] [depth= 1] . ( 2 sec) [ -3512.8935] [ 370] [depth= 6] . ( 2 sec) [ -3500.3422] [ 368] [depth= 4] . ( 3 sec) [ -3487.8572] [ 371] [depth= 1] . ( 3 sec) [ -3437.2073] [ 363] [depth= 6] . ( 3 sec) [ -3433.0277] [ 362] [depth= 1] . ( 3 sec) [ -3424.3430] [ 362] [depth= 1] . ( 3 sec) [ -3420.5096] [ 360] [depth= 2] . ( 3 sec) [ -3417.9228] [ 358] [depth= 2] . ( 5 sec) [ -3409.4911] [ 358] [depth= 2] . ( 6 sec) [ -3398.2898] [ 356] [depth= 3] . ( 6 sec) [ -3389.2386] [ 355] [depth= 1] . ( 6 sec) [ -3371.3141] [ 357] [depth= 3] . ( 6 sec) [ -3358.7933] [ 354] [depth= 4] . ( 7 sec) [ -3348.3955] [ 350] [depth= 3] . ( 7 sec) [ -3339.6942] [ 349] [depth= 2] . ( 7 sec) [ -3338.8478] [ 349] [depth= 2] . ( 7 sec) [ -3311.8246] [ 339] [depth= 7] . ( 8 sec) [ -3290.6164] [ 335] [depth= 6] . ( 8 sec) [ -3275.4615] [ 330] [depth= 3] . ( 8 sec) [ -3275.1831] [ 331] [depth= 1] . ( 8 sec) [ -3272.9785] [ 330] [depth= 1] . ( 8 sec) [ -3272.2743] [ 331] [depth= 3] . ( 8 sec) [ -3268.9102] [ 330] [depth= 1] . ( 9 sec) [ -3255.0737] [ 327] [depth= 2] . ( 9 sec) [ -3246.0478] [ 324] [depth= 1] . ( 9 sec) [ -3225.9334] [ 319] [depth= 2] . ( 9 sec) [ -3196.6158] [ 319] [depth= 1] . ( 10 sec) [ -3193.2529] [ 318] [depth= 4] . ( 10 sec) [ -3191.5754] [ 318] [depth= 1] . ( 11 sec) [ -3188.8737] [ 318] [depth= 1] . ( 11 sec) [ -3183.7304] [ 316] [depth= 2] . ( 11 sec) [ -3183.5923] [ 316] [depth= 1] . ( 12 sec) [ -3183.2608] [ 316] [depth= 1] . ( 14 sec) [ -3174.9994] [Branch lengths ] . ( 14 sec) [ -3165.0420] [Alpha ][ 0.269923] . ( 19 sec) [ -3164.7130] [ 317] [depth= 1] . ( 22 sec) [ -3161.4135] [ 317] [depth= 2] . ( 22 sec) [ -3161.2946] [ 317] [depth= 2] . ( 22 sec) [ -3159.1931] [ 316] [depth= 1] . ( 32 sec) [ -3158.8742] [ 315] [depth= 3] . ( 33 sec) [ -3158.3238] [ 316] [depth= 1] . ( 41 sec) [ -3157.1774] [ 316] [depth= 2] . ( 54 sec) [ -3157.1091] [ 316] [depth= 1] . ( 54 sec) [ -3156.2036] [ 320] [depth= 3] . ( 56 sec) [ -3153.1183] [Branch lengths ] . ( 56 sec) [ -3153.1183] [Alpha ][ 0.269923] . ( 112 sec) [ -3153.0779] [Branch lengths ] . ( 112 sec) [ -3153.0779] [Topology ] . ( 113 sec) [ -3153.0778] [Topology ] . ( 113 sec) [ -3153.0778] [Alpha ][ 0.269653] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3153.077819. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3994.3769] [Alpha ][ 0.500960] . ( 0 sec) [ -3947.7966] [ 396] [depth= 8] . ( 0 sec) [ -3896.2584] [ 392] [depth= 10] . ( 1 sec) [ -3837.6692] [ 391] [depth= 1] . ( 1 sec) [ -3770.7535] [ 390] [depth= 3] . ( 1 sec) [ -3740.7227] [ 385] [depth= 2] . ( 1 sec) [ -3733.9019] [ 384] [depth= 2] . ( 1 sec) [ -3713.7401] [ 383] [depth= 2] . ( 1 sec) [ -3606.3454] [ 380] [depth= 5] . ( 1 sec) [ -3591.7493] [ 375] [depth= 2] . ( 2 sec) [ -3564.0863] [ 371] [depth= 1] . ( 2 sec) [ -3562.6643] [ 371] [depth= 2] . ( 2 sec) [ -3557.5427] [ 368] [depth= 4] . ( 2 sec) [ -3504.7811] [ 367] [depth= 2] . ( 2 sec) [ -3501.7344] [ 368] [depth= 6] . ( 2 sec) [ -3458.1761] [ 356] [depth= 5] . ( 2 sec) [ -3453.6993] [ 355] [depth= 2] . ( 3 sec) [ -3436.9465] [ 353] [depth= 2] . ( 3 sec) [ -3432.5293] [ 353] [depth= 1] . ( 3 sec) [ -3402.5182] [ 351] [depth= 3] . ( 3 sec) [ -3383.2329] [ 350] [depth= 1] . ( 3 sec) [ -3382.6818] [ 353] [depth= 3] . ( 4 sec) [ -3362.4881] [ 350] [depth= 4] . ( 4 sec) [ -3343.8518] [ 347] [depth= 2] . ( 4 sec) [ -3341.3253] [ 343] [depth= 6] . ( 4 sec) [ -3335.2687] [ 343] [depth= 8] . ( 4 sec) [ -3332.6051] [ 344] [depth= 7] . ( 4 sec) [ -3323.8452] [ 342] [depth= 1] . ( 5 sec) [ -3297.6127] [ 335] [depth= 9] . ( 5 sec) [ -3294.2196] [ 331] [depth= 8] . ( 5 sec) [ -3292.4413] [ 333] [depth= 2] . ( 5 sec) [ -3254.7406] [ 330] [depth= 1] . ( 5 sec) [ -3242.5157] [ 328] [depth= 3] . ( 5 sec) [ -3235.5781] [ 326] [depth= 1] . ( 6 sec) [ -3219.0207] [ 323] [depth= 6] . ( 6 sec) [ -3218.6942] [ 324] [depth= 1] . ( 8 sec) [ -3215.0618] [ 324] [depth= 1] . ( 9 sec) [ -3214.1602] [ 326] [depth= 3] . ( 9 sec) [ -3198.7266] [ 322] [depth= 7] . ( 9 sec) [ -3191.2230] [ 320] [depth= 5] . ( 10 sec) [ -3189.4272] [ 320] [depth= 1] . ( 10 sec) [ -3187.2119] [ 319] [depth= 1] . ( 12 sec) [ -3181.4310] [ 318] [depth= 3] . ( 13 sec) [ -3177.7411] [ 319] [depth= 1] . ( 13 sec) [ -3176.9001] [ 319] [depth= 1] . ( 14 sec) [ -3171.0634] [Branch lengths ] . ( 14 sec) [ -3161.2199] [Alpha ][ 0.271384] . ( 15 sec) [ -3159.8780] [ 317] [depth= 1] . ( 16 sec) [ -3155.4087] [ 315] [depth= 1] . ( 17 sec) [ -3153.6147] [ 315] [depth= 1] . ( 17 sec) [ -3152.7241] [ 314] [depth= 1] . ( 18 sec) [ -3149.9314] [ 314] [depth= 1] . ( 19 sec) [ -3149.4530] [ 314] [depth= 1] . ( 20 sec) [ -3149.0105] [ 313] [depth= 2] . ( 22 sec) [ -3148.2481] [ 314] [depth= 1] . ( 25 sec) [ -3148.0505] [ 313] [depth= 1] . ( 33 sec) [ -3147.7665] [ 313] [depth= 2] . ( 33 sec) [ -3147.7214] [ 314] [depth= 1] . ( 41 sec) [ -3147.1276] [Branch lengths ] . ( 42 sec) [ -3147.1271] [Alpha ][ 0.270102] . ( 80 sec) [ -3147.1134] [Branch lengths ] . ( 80 sec) [ -3147.1134] [Topology ] . ( 81 sec) [ -3147.1126] [Topology ] . ( 81 sec) [ -3147.1124] [Alpha ][ 0.269331] . Checking for NNIs, optimizing five branches... . ( 88 sec) [ -3147.0653] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3147.065291. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4030.9266] [Alpha ][ 0.500960] . ( 0 sec) [ -3967.0192] [ 400] [depth= 9] . ( 0 sec) [ -3942.4157] [ 397] [depth= 7] . ( 1 sec) [ -3892.4949] [ 395] [depth= 1] . ( 1 sec) [ -3857.5323] [ 391] [depth= 4] . ( 1 sec) [ -3851.2972] [ 389] [depth= 1] . ( 1 sec) [ -3662.7413] [ 386] [depth= 4] . ( 1 sec) [ -3642.9067] [ 381] [depth= 1] . ( 1 sec) [ -3606.1871] [ 379] [depth= 1] . ( 1 sec) [ -3591.1013] [ 377] [depth= 1] . ( 2 sec) [ -3568.8472] [ 375] [depth= 3] . ( 2 sec) [ -3531.3534] [ 374] [depth= 4] . ( 2 sec) [ -3503.0624] [ 363] [depth= 1] . ( 2 sec) [ -3481.9261] [ 361] [depth= 1] . ( 2 sec) [ -3434.1480] [ 360] [depth= 2] . ( 2 sec) [ -3423.1147] [ 359] [depth= 2] . ( 2 sec) [ -3414.7302] [ 357] [depth= 3] . ( 3 sec) [ -3384.9087] [ 355] [depth= 2] . ( 3 sec) [ -3372.6974] [ 351] [depth= 4] . ( 3 sec) [ -3365.8050] [ 349] [depth= 1] . ( 3 sec) [ -3360.6100] [ 349] [depth= 6] . ( 3 sec) [ -3355.8623] [ 348] [depth= 3] . ( 3 sec) [ -3336.7136] [ 345] [depth= 2] . ( 3 sec) [ -3335.9557] [ 344] [depth= 2] . ( 4 sec) [ -3332.5806] [ 343] [depth= 1] . ( 4 sec) [ -3315.2227] [ 337] [depth= 4] . ( 4 sec) [ -3280.7090] [ 329] [depth= 4] . ( 4 sec) [ -3277.1864] [ 329] [depth= 1] . ( 4 sec) [ -3273.7188] [ 328] [depth= 1] . ( 7 sec) [ -3256.4208] [ 332] [depth= 1] . ( 7 sec) [ -3251.5506] [ 328] [depth= 1] . ( 8 sec) [ -3237.0586] [ 326] [depth= 3] . ( 9 sec) [ -3236.3345] [ 326] [depth= 1] . ( 10 sec) [ -3236.2494] [ 326] [depth= 1] . ( 10 sec) [ -3236.2206] [ 326] [depth= 1] . ( 11 sec) [ -3222.2194] [ 323] [depth= 1] . ( 11 sec) [ -3220.9448] [ 323] [depth= 1] . ( 11 sec) [ -3215.7177] [ 321] [depth= 2] . ( 13 sec) [ -3207.6996] [ 320] [depth= 4] . ( 13 sec) [ -3199.0255] [ 318] [depth= 2] . ( 16 sec) [ -3193.3248] [ 317] [depth= 5] . ( 17 sec) [ -3175.6846] [Branch lengths ] . ( 17 sec) [ -3165.9147] [Alpha ][ 0.274476] . ( 18 sec) [ -3165.5069] [ 317] [depth= 2] . ( 19 sec) [ -3165.4831] [ 317] [depth= 1] . ( 19 sec) [ -3164.7707] [ 316] [depth= 1] . ( 20 sec) [ -3164.0142] [ 315] [depth= 1] . ( 21 sec) [ -3158.8013] [ 315] [depth= 4] . ( 23 sec) [ -3156.9308] [ 314] [depth= 1] . ( 37 sec) [ -3156.2822] [ 318] [depth= 3] . ( 37 sec) [ -3156.0090] [ 317] [depth= 4] . ( 49 sec) [ -3155.6389] [ 316] [depth= 1] . ( 51 sec) [ -3153.8020] [Branch lengths ] . ( 51 sec) [ -3153.7966] [Alpha ][ 0.270942] . ( 53 sec) [ -3149.6029] [ 313] [depth= 2] . ( 62 sec) [ -3149.2119] [ 313] [depth= 1] . ( 88 sec) [ -3147.0907] [Branch lengths ] . ( 88 sec) [ -3147.0907] [Alpha ][ 0.270571] . ( 126 sec) [ -3147.0674] [Branch lengths ] . ( 126 sec) [ -3147.0674] [Topology ] . ( 127 sec) [ -3147.0658] [Topology ] . ( 128 sec) [ -3147.0653] [Topology ] . ( 128 sec) [ -3147.0649] [Alpha ][ 0.269492] . ( 128 sec) [ -3147.0649] [Topology ] . ( 129 sec) [ -3147.0646] [Topology ] . ( 129 sec) [ -3147.0646] [Alpha ][ 0.269492] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3147.064630. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3841.8858] [Alpha ][ 0.500960] . ( 1 sec) [ -3788.9494] [ 386] [depth= 7] . ( 1 sec) [ -3755.3328] [ 379] [depth= 4] . ( 1 sec) [ -3662.1033] [ 366] [depth= 3] . ( 1 sec) [ -3659.2049] [ 365] [depth= 1] . ( 1 sec) [ -3604.0736] [ 359] [depth= 4] . ( 1 sec) [ -3597.8289] [ 358] [depth= 1] . ( 2 sec) [ -3561.1893] [ 354] [depth= 5] . ( 2 sec) [ -3550.0498] [ 351] [depth= 7] . ( 2 sec) [ -3543.1685] [ 351] [depth= 1] . ( 2 sec) [ -3542.7140] [ 352] [depth= 1] . ( 4 sec) [ -3493.8504] [ 348] [depth= 5] . ( 4 sec) [ -3485.0575] [ 345] [depth= 6] . ( 4 sec) [ -3479.2813] [ 344] [depth= 2] . ( 4 sec) [ -3456.9801] [ 343] [depth= 3] . ( 5 sec) [ -3439.3594] [ 342] [depth= 2] . ( 5 sec) [ -3437.4890] [ 342] [depth= 1] . ( 5 sec) [ -3417.0856] [ 342] [depth= 1] . ( 5 sec) [ -3417.0526] [ 343] [depth= 1] . ( 6 sec) [ -3395.1941] [ 336] [depth= 5] . ( 6 sec) [ -3395.0193] [ 336] [depth= 2] . ( 6 sec) [ -3390.2820] [ 335] [depth= 1] . ( 7 sec) [ -3390.1181] [ 335] [depth= 1] . ( 8 sec) [ -3374.9727] [ 332] [depth= 3] . ( 8 sec) [ -3353.1827] [ 334] [depth= 1] . ( 8 sec) [ -3353.1517] [ 337] [depth= 2] . ( 8 sec) [ -3331.4991] [ 327] [depth= 4] . ( 9 sec) [ -3317.9907] [ 324] [depth= 1] . ( 9 sec) [ -3317.4478] [ 323] [depth= 1] . ( 10 sec) [ -3272.8343] [ 328] [depth= 4] . ( 10 sec) [ -3259.5001] [ 326] [depth= 3] . ( 10 sec) [ -3243.4799] [ 322] [depth= 1] . ( 11 sec) [ -3214.2157] [ 324] [depth= 2] . ( 12 sec) [ -3212.4297] [ 322] [depth= 2] . ( 12 sec) [ -3211.0586] [ 323] [depth= 1] . ( 12 sec) [ -3210.5302] [ 324] [depth= 1] . ( 12 sec) [ -3209.8953] [ 322] [depth= 5] . ( 16 sec) [ -3207.3633] [ 322] [depth= 1] . ( 17 sec) [ -3197.5477] [Branch lengths ] . ( 17 sec) [ -3186.6133] [Alpha ][ 0.263635] . ( 18 sec) [ -3179.9195] [ 319] [depth= 2] . ( 21 sec) [ -3179.8944] [ 321] [depth= 1] . ( 21 sec) [ -3176.8152] [ 319] [depth= 2] . ( 21 sec) [ -3176.4166] [ 319] [depth= 1] . ( 22 sec) [ -3173.3652] [ 318] [depth= 1] . ( 27 sec) [ -3170.2486] [ 318] [depth= 2] . ( 27 sec) [ -3169.8583] [ 318] [depth= 2] . ( 27 sec) [ -3167.8373] [ 317] [depth= 1] . ( 33 sec) [ -3163.2488] [ 316] [depth= 1] . ( 35 sec) [ -3162.5702] [ 316] [depth= 1] . ( 35 sec) [ -3161.1710] [ 317] [depth= 1] . ( 36 sec) [ -3159.3772] [ 318] [depth= 2] . ( 36 sec) [ -3157.7931] [ 317] [depth= 1] . ( 39 sec) [ -3155.8755] [ 315] [depth= 2] . ( 41 sec) [ -3152.9083] [ 315] [depth= 1] . ( 46 sec) [ -3149.1868] [Branch lengths ] . ( 46 sec) [ -3149.1674] [Alpha ][ 0.270475] . ( 52 sec) [ -3147.3968] [ 314] [depth= 3] . ( 86 sec) [ -3147.1151] [Branch lengths ] . ( 86 sec) [ -3147.1146] [Alpha ][ 0.269242] . ( 128 sec) [ -3147.1121] [Branch lengths ] . ( 128 sec) [ -3147.1121] [Topology ] . ( 129 sec) [ -3147.1120] [Topology ] . ( 129 sec) [ -3147.1120] [Alpha ][ 0.269242] . Checking for NNIs, optimizing five branches... . ( 136 sec) [ -3147.0646] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3147.064578. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3893.6843] [Alpha ][ 0.500960] . ( 0 sec) [ -3819.7155] [ 396] [depth= 6] . ( 1 sec) [ -3738.9853] [ 384] [depth= 4] . ( 1 sec) [ -3725.5210] [ 382] [depth= 2] . ( 1 sec) [ -3695.2722] [ 380] [depth= 2] . ( 1 sec) [ -3676.6507] [ 374] [depth= 5] . ( 1 sec) [ -3651.9410] [ 375] [depth= 4] . ( 1 sec) [ -3633.7227] [ 373] [depth= 5] . ( 1 sec) [ -3585.0426] [ 368] [depth= 4] . ( 2 sec) [ -3583.9423] [ 373] [depth= 9] . ( 2 sec) [ -3564.3120] [ 374] [depth= 4] . ( 2 sec) [ -3549.7078] [ 371] [depth= 3] . ( 2 sec) [ -3527.2370] [ 370] [depth= 1] . ( 2 sec) [ -3414.3961] [ 361] [depth= 7] . ( 2 sec) [ -3408.6582] [ 360] [depth= 2] . ( 2 sec) [ -3400.8686] [ 359] [depth= 2] . ( 3 sec) [ -3381.8962] [ 354] [depth= 5] . ( 4 sec) [ -3373.0594] [ 359] [depth= 5] . ( 4 sec) [ -3370.1320] [ 359] [depth= 1] . ( 4 sec) [ -3369.4427] [ 359] [depth= 1] . ( 4 sec) [ -3350.7117] [ 355] [depth= 4] . ( 4 sec) [ -3347.6616] [ 354] [depth= 4] . ( 5 sec) [ -3346.0593] [ 351] [depth= 2] . ( 5 sec) [ -3339.7242] [ 349] [depth= 2] . ( 5 sec) [ -3338.9688] [ 349] [depth= 1] . ( 5 sec) [ -3283.1669] [ 336] [depth= 5] . ( 6 sec) [ -3282.9842] [ 336] [depth= 1] . ( 6 sec) [ -3265.2105] [ 332] [depth= 2] . ( 6 sec) [ -3263.5730] [ 333] [depth= 2] . ( 6 sec) [ -3222.6522] [ 322] [depth= 9] . ( 7 sec) [ -3220.8182] [ 324] [depth= 4] . ( 8 sec) [ -3220.1839] [ 322] [depth= 2] . ( 8 sec) [ -3208.0658] [ 317] [depth= 4] . ( 9 sec) [ -3207.7653] [ 318] [depth= 1] . ( 9 sec) [ -3195.2138] [ 318] [depth= 2] . ( 9 sec) [ -3186.7482] [ 317] [depth= 2] . ( 9 sec) [ -3186.1037] [ 317] [depth= 2] . ( 10 sec) [ -3175.3721] [ 315] [depth= 1] . ( 10 sec) [ -3174.2748] [ 315] [depth= 1] . ( 11 sec) [ -3171.0256] [ 315] [depth= 1] . ( 13 sec) [ -3170.7241] [ 315] [depth= 2] . ( 16 sec) [ -3165.9222] [Branch lengths ] . ( 16 sec) [ -3156.6226] [Alpha ][ 0.274707] . ( 29 sec) [ -3156.0445] [ 315] [depth= 1] . ( 33 sec) [ -3155.7145] [ 319] [depth= 5] . ( 46 sec) [ -3155.6806] [ 318] [depth= 2] . ( 62 sec) [ -3152.3903] [Branch lengths ] . ( 62 sec) [ -3152.3865] [Alpha ][ 0.271511] . ( 111 sec) [ -3152.2306] [Branch lengths ] . ( 111 sec) [ -3152.2306] [Topology ] . ( 112 sec) [ -3152.2301] [Topology ] . ( 112 sec) [ -3152.2301] [Alpha ][ 0.271511] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3152.230135. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3189.9244] [Alpha ][ 0.500960] . ( 0 sec) [ -3189.9244] [Topology ] . ( 1 sec) [ -3169.1490] [Topology ] . ( 2 sec) [ -3166.4088] [Topology ] . ( 3 sec) [ -3166.3187] [Topology ] . ( 4 sec) [ -3165.6320] [Topology ] . ( 5 sec) [ -3165.9418] [Topology ] . Moving backward . ( 5 sec) [ -3164.4686] [Topology ] . ( 6 sec) [ -3164.3597] [Topology ] . ( 7 sec) [ -3164.3433] [Topology ] . ( 8 sec) [ -3164.3398] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -3155.1388] [Alpha ][ 0.275768] . ( 15 sec) [ -3155.1388] [Topology ] . ( 16 sec) [ -3155.0993] [Topology ] . ( 17 sec) [ -3155.0947] [Topology ] . ( 18 sec) [ -3155.0933] [Topology ] . ( 19 sec) [ -3155.0929] [Topology ] . Checking for NNIs, optimizing five branches... . ( 25 sec) [ -3155.0918] [Alpha ][ 0.274054] . ( 25 sec) [ -3155.0918] [Topology ] . ( 26 sec) [ -3155.0915] [Topology ] . Checking for NNIs, optimizing five branches... . ( 32 sec) [ -3155.0915] [Alpha ][ 0.274054] . ( 32 sec) [ -3155.0915] [Topology ] . ( 33 sec) [ -3155.0913] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 46 sec) [ -3189.9244] [Alpha ][ 0.500960] . ( 50 sec) [ -3187.2806] [ 315] [depth= 1] . ( 54 sec) [ -3185.8706] [ 319] [depth= 4] . ( 54 sec) [ -3184.0076] [ 319] [depth= 1] . ( 54 sec) [ -3182.5111] [ 319] [depth= 1] . ( 55 sec) [ -3181.7331] [ 319] [depth= 1] . ( 57 sec) [ -3181.5180] [ 319] [depth= 1] . ( 57 sec) [ -3181.2264] [ 319] [depth= 1] . ( 58 sec) [ -3181.0679] [ 319] [depth= 1] . ( 58 sec) [ -3180.6103] [ 320] [depth= 2] . ( 58 sec) [ -3176.1281] [ 320] [depth= 4] . ( 65 sec) [ -3173.0154] [ 320] [depth= 1] . ( 65 sec) [ -3172.6462] [ 320] [depth= 1] . ( 65 sec) [ -3172.3535] [ 320] [depth= 1] . ( 65 sec) [ -3171.5527] [ 320] [depth= 1] . ( 66 sec) [ -3170.6153] [ 320] [depth= 1] . ( 80 sec) [ -3163.4617] [Branch lengths ] . ( 80 sec) [ -3153.5686] [Alpha ][ 0.268252] . ( 105 sec) [ -3153.5475] [ 320] [depth= 1] . ( 135 sec) [ -3153.0856] [Branch lengths ] . ( 135 sec) [ -3153.0852] [Alpha ][ 0.269228] . ( 135 sec) [ -3153.0852] [Topology ] . ( 136 sec) [ -3153.0791] [Topology ] . ( 137 sec) [ -3153.0783] [Topology ] . ( 137 sec) [ -3153.0783] [Alpha ][ 0.269517] . ( 137 sec) [ -3153.0783] [Topology ] . ( 138 sec) [ -3153.0780] [Topology ] . ( 138 sec) [ -3153.0780] [Alpha ][ 0.269517] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3155.091315 . Log likelihood obtained after SPR moves : -3153.078044 . Log likelihood of the current tree: -3153.078044. . Printing the most likely tree in file 'proteic_M1508_22x431_2003.phy_phyml_tree.txt'... . Best log likelihood : -3147.064578 . Time used 0h2m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 749.17user 0.00system 12:38.08elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps