.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2479_30x627_2005.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... . 521 patterns found. (out of a total of 627 sites) . 123 sites without polymorphism (19.62%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 37Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23009.6978] [Alpha ][ 0.500960] . ( 2 sec) [ -22596.8178] [ 3978] [depth= 2] . ( 3 sec) [ -22309.2221] [ 3919] [depth= 5] . ( 3 sec) [ -22132.5007] [ 3904] [depth= 2] . ( 3 sec) [ -21951.7280] [ 3878] [depth= 4] . ( 4 sec) [ -21928.8825] [ 3871] [depth= 1] . ( 4 sec) [ -21756.6749] [ 3869] [depth= 5] . ( 5 sec) [ -21743.8512] [ 3875] [depth= 2] . ( 5 sec) [ -21576.2658] [ 3861] [depth= 5] . ( 6 sec) [ -21508.3828] [ 3844] [depth= 3] . ( 6 sec) [ -21381.6900] [ 3843] [depth= 2] . ( 7 sec) [ -21273.9820] [ 3821] [depth= 1] . ( 7 sec) [ -21157.6078] [ 3810] [depth= 1] . ( 7 sec) [ -21096.1587] [ 3793] [depth= 1] . ( 8 sec) [ -20855.0965] [ 3774] [depth= 3] . ( 8 sec) [ -20738.1262] [ 3746] [depth= 2] . ( 9 sec) [ -20683.9568] [ 3738] [depth= 3] . ( 9 sec) [ -20678.1265] [ 3739] [depth= 1] . ( 10 sec) [ -20549.3797] [ 3740] [depth= 7] . ( 10 sec) [ -20533.8566] [ 3736] [depth= 1] . ( 11 sec) [ -20527.8039] [ 3736] [depth= 2] . ( 12 sec) [ -20453.5889] [ 3721] [depth= 1] . ( 12 sec) [ -20436.8512] [ 3721] [depth= 7] . ( 13 sec) [ -20336.2631] [ 3689] [depth= 3] . ( 13 sec) [ -20301.8569] [ 3670] [depth= 1] . ( 14 sec) [ -20198.0931] [ 3647] [depth= 8] . ( 15 sec) [ -20195.9882] [ 3649] [depth= 1] . ( 15 sec) [ -20156.1768] [ 3643] [depth= 6] . ( 16 sec) [ -20150.3093] [ 3641] [depth= 1] . ( 17 sec) [ -20062.9783] [ 3641] [depth= 1] . ( 17 sec) [ -19949.6453] [ 3606] [depth= 7] . ( 18 sec) [ -19928.7468] [ 3598] [depth= 4] . ( 18 sec) [ -19912.1984] [ 3591] [depth= 2] . ( 19 sec) [ -19870.5698] [ 3586] [depth= 1] . ( 20 sec) [ -19684.2990] [ 3523] [depth= 6] . ( 20 sec) [ -19672.8101] [ 3523] [depth= 6] . ( 21 sec) [ -19583.2465] [ 3504] [depth= 1] . ( 22 sec) [ -19582.4864] [ 3505] [depth= 1] . ( 23 sec) [ -19408.3528] [ 3475] [depth= 6] . ( 23 sec) [ -19332.0155] [ 3484] [depth= 1] . ( 24 sec) [ -19304.6149] [ 3475] [depth= 1] . ( 24 sec) [ -19163.3921] [ 3423] [depth= 4] . ( 25 sec) [ -19150.7785] [ 3422] [depth= 2] . ( 26 sec) [ -19146.1588] [ 3426] [depth= 1] . ( 26 sec) [ -19106.3494] [ 3419] [depth= 5] . ( 27 sec) [ -19078.8638] [ 3408] [depth= 2] . ( 27 sec) [ -19074.1426] [ 3401] [depth= 2] . ( 28 sec) [ -18887.5169] [ 3392] [depth= 1] . ( 28 sec) [ -18869.3448] [ 3389] [depth= 2] . ( 29 sec) [ -18753.7134] [ 3374] [depth= 1] . ( 29 sec) [ -18654.0435] [ 3382] [depth= 1] . ( 30 sec) [ -18607.5732] [ 3376] [depth= 6] . ( 30 sec) [ -18503.0837] [ 3344] [depth= 1] . ( 31 sec) [ -18465.3250] [ 3342] [depth= 1] . ( 32 sec) [ -18439.8959] [ 3335] [depth= 1] . ( 32 sec) [ -18435.4192] [ 3332] [depth= 2] . ( 33 sec) [ -18429.1769] [ 3334] [depth= 1] . ( 35 sec) [ -18361.7576] [ 3326] [depth= 4] . ( 36 sec) [ -18349.4266] [ 3319] [depth= 1] . ( 36 sec) [ -18337.6531] [ 3320] [depth= 1] . ( 37 sec) [ -18300.2757] [ 3317] [depth= 1] . ( 37 sec) [ -18299.1206] [ 3315] [depth= 1] . ( 38 sec) [ -18291.2844] [ 3316] [depth= 1] . ( 38 sec) [ -18246.5255] [ 3299] [depth= 6] . ( 39 sec) [ -18241.7418] [ 3299] [depth= 1] . ( 40 sec) [ -18163.7911] [Branch lengths ] . ( 41 sec) [ -18150.7113] [Alpha ][ 0.660370] . ( 42 sec) [ -18120.9638] [ 3281] [depth= 1] . ( 45 sec) [ -18120.8620] [ 3278] [depth= 2] . ( 48 sec) [ -18120.8040] [ 3279] [depth= 1] . ( 50 sec) [ -18118.7380] [ 3277] [depth= 1] . ( 51 sec) [ -18107.8107] [ 3274] [depth= 1] . ( 58 sec) [ -18107.6335] [ 3279] [depth= 2] . ( 59 sec) [ -18105.9012] [ 3279] [depth= 2] . ( 62 sec) [ -18102.1184] [ 3278] [depth= 3] . ( 63 sec) [ -18101.9231] [ 3282] [depth= 1] . ( 67 sec) [ -18101.6164] [ 3283] [depth= 1] . ( 67 sec) [ -18099.3030] [ 3273] [depth= 1] . ( 68 sec) [ -18095.3417] [ 3268] [depth= 1] . ( 72 sec) [ -18094.5845] [ 3271] [depth= 1] . ( 74 sec) [ -18093.4470] [ 3268] [depth= 1] . ( 76 sec) [ -18092.9877] [ 3268] [depth= 1] . ( 77 sec) [ -18092.8887] [ 3267] [depth= 1] . ( 79 sec) [ -18090.7068] [ 3271] [depth= 3] . ( 81 sec) [ -18072.6530] [Branch lengths ] . ( 81 sec) [ -18071.5817] [Alpha ][ 0.715096] . ( 89 sec) [ -18069.5303] [ 3274] [depth= 1] . ( 90 sec) [ -18066.3263] [ 3269] [depth= 5] . ( 100 sec) [ -18060.4769] [ 3269] [depth= 1] . ( 107 sec) [ -18060.2207] [ 3270] [depth= 1] . ( 109 sec) [ -18059.1691] [ 3267] [depth= 1] . ( 121 sec) [ -18055.2153] [Branch lengths ] . ( 122 sec) [ -18055.0874] [Alpha ][ 0.734664] . ( 169 sec) [ -18054.4920] [Branch lengths ] . ( 169 sec) [ -18054.4920] [Topology ] . ( 172 sec) [ -18054.4102] [Topology ] . ( 175 sec) [ -18054.3801] [Topology ] . ( 178 sec) [ -18054.3643] [Topology ] . ( 181 sec) [ -18054.3557] [Topology ] . ( 184 sec) [ -18054.3511] [Topology ] . ( 188 sec) [ -18054.3486] [Topology ] . ( 188 sec) [ -18054.2619] [Alpha ][ 0.751647] . ( 188 sec) [ -18054.2619] [Topology ] . ( 191 sec) [ -18054.2480] [Topology ] . ( 194 sec) [ -18054.2412] [Topology ] . ( 197 sec) [ -18054.2375] [Topology ] . ( 200 sec) [ -18054.2356] [Topology ] . ( 204 sec) [ -18054.2345] [Topology ] . ( 207 sec) [ -18054.2339] [Topology ] . ( 207 sec) [ -18054.2315] [Alpha ][ 0.754421] . ( 207 sec) [ -18054.2315] [Topology ] . ( 210 sec) [ -18054.2306] [Topology ] . ( 211 sec) [ -18054.2306] [Alpha ][ 0.754421] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -18054.230598. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23158.0749] [Alpha ][ 0.500960] . ( 2 sec) [ -22952.9872] [ 3990] [depth= 8] . ( 2 sec) [ -22704.0904] [ 3939] [depth= 6] . ( 3 sec) [ -22307.8851] [ 3924] [depth= 2] . ( 3 sec) [ -22199.7561] [ 3895] [depth= 1] . ( 3 sec) [ -21918.7522] [ 3873] [depth= 6] . ( 4 sec) [ -21869.8952] [ 3871] [depth= 1] . ( 4 sec) [ -21836.6614] [ 3856] [depth= 3] . ( 5 sec) [ -21794.2884] [ 3838] [depth= 2] . ( 5 sec) [ -21561.7987] [ 3806] [depth= 5] . ( 6 sec) [ -21361.6923] [ 3763] [depth= 3] . ( 6 sec) [ -21339.3294] [ 3761] [depth= 1] . ( 6 sec) [ -21223.5660] [ 3731] [depth= 1] . ( 7 sec) [ -21109.2622] [ 3708] [depth= 4] . ( 7 sec) [ -21064.5853] [ 3702] [depth= 2] . ( 8 sec) [ -21034.2345] [ 3700] [depth= 2] . ( 8 sec) [ -20929.0248] [ 3681] [depth= 1] . ( 9 sec) [ -20916.1385] [ 3672] [depth= 1] . ( 9 sec) [ -20763.1894] [ 3666] [depth= 2] . ( 10 sec) [ -20633.9019] [ 3664] [depth= 1] . ( 10 sec) [ -20462.9139] [ 3659] [depth= 4] . ( 11 sec) [ -20338.5727] [ 3662] [depth= 1] . ( 11 sec) [ -20178.2823] [ 3615] [depth= 8] . ( 12 sec) [ -20146.7092] [ 3613] [depth= 1] . ( 12 sec) [ -19911.3795] [ 3584] [depth= 5] . ( 13 sec) [ -19823.2211] [ 3577] [depth= 4] . ( 14 sec) [ -19739.9105] [ 3561] [depth= 7] . ( 14 sec) [ -19734.0942] [ 3564] [depth= 1] . ( 15 sec) [ -19619.5305] [ 3559] [depth= 5] . ( 15 sec) [ -19529.0092] [ 3544] [depth= 4] . ( 16 sec) [ -19437.1021] [ 3540] [depth= 3] . ( 16 sec) [ -19432.4602] [ 3535] [depth= 2] . ( 17 sec) [ -19385.1403] [ 3523] [depth= 1] . ( 17 sec) [ -19299.4633] [ 3512] [depth= 6] . ( 18 sec) [ -19202.0194] [ 3502] [depth= 2] . ( 19 sec) [ -19164.8014] [ 3494] [depth= 1] . ( 19 sec) [ -19080.5398] [ 3465] [depth= 1] . ( 19 sec) [ -19025.9282] [ 3455] [depth= 2] . ( 20 sec) [ -18977.3298] [ 3455] [depth= 1] . ( 20 sec) [ -18971.4017] [ 3458] [depth= 6] . ( 21 sec) [ -18969.8926] [ 3457] [depth= 4] . ( 22 sec) [ -18961.8820] [ 3456] [depth= 10] . ( 23 sec) [ -18873.1803] [ 3423] [depth= 3] . ( 23 sec) [ -18753.3684] [ 3407] [depth= 7] . ( 24 sec) [ -18746.9977] [ 3418] [depth= 1] . ( 25 sec) [ -18745.1927] [ 3414] [depth= 1] . ( 25 sec) [ -18744.1388] [ 3408] [depth= 7] . ( 26 sec) [ -18717.0242] [ 3401] [depth= 1] . ( 26 sec) [ -18535.4351] [ 3358] [depth= 8] . ( 27 sec) [ -18533.1316] [ 3348] [depth= 1] . ( 27 sec) [ -18517.5533] [ 3346] [depth= 3] . ( 27 sec) [ -18497.9515] [ 3343] [depth= 1] . ( 28 sec) [ -18477.9657] [ 3340] [depth= 5] . ( 29 sec) [ -18466.5545] [ 3339] [depth= 1] . ( 30 sec) [ -18466.2624] [ 3342] [depth= 1] . ( 30 sec) [ -18461.5657] [ 3343] [depth= 1] . ( 31 sec) [ -18454.0173] [ 3337] [depth= 1] . ( 31 sec) [ -18438.7935] [ 3324] [depth= 3] . ( 35 sec) [ -18272.7069] [ 3289] [depth= 1] . ( 35 sec) [ -18271.5555] [ 3288] [depth= 1] . ( 36 sec) [ -18267.9528] [ 3287] [depth= 1] . ( 36 sec) [ -18244.1150] [ 3282] [depth= 1] . ( 37 sec) [ -18239.1109] [ 3285] [depth= 1] . ( 38 sec) [ -18168.9394] [Branch lengths ] . ( 39 sec) [ -18153.3302] [Alpha ][ 0.676313] . ( 40 sec) [ -18130.6392] [ 3274] [depth= 3] . ( 41 sec) [ -18129.7879] [ 3273] [depth= 2] . ( 44 sec) [ -18105.0611] [ 3263] [depth= 1] . ( 47 sec) [ -18104.7221] [ 3267] [depth= 2] . ( 48 sec) [ -18096.1239] [ 3263] [depth= 1] . ( 49 sec) [ -18095.2537] [ 3268] [depth= 2] . ( 54 sec) [ -18094.5156] [ 3269] [depth= 1] . ( 55 sec) [ -18092.7250] [ 3272] [depth= 1] . ( 56 sec) [ -18089.8926] [ 3274] [depth= 1] . ( 56 sec) [ -18082.5740] [ 3265] [depth= 3] . ( 65 sec) [ -18077.6771] [ 3263] [depth= 1] . ( 67 sec) [ -18077.2597] [ 3267] [depth= 1] . ( 68 sec) [ -18076.3625] [ 3267] [depth= 1] . ( 70 sec) [ -18073.5143] [ 3269] [depth= 1] . ( 73 sec) [ -18054.9621] [Branch lengths ] . ( 74 sec) [ -18054.0891] [Alpha ][ 0.726621] . ( 124 sec) [ -18052.4685] [Branch lengths ] . ( 124 sec) [ -18052.4685] [Topology ] . ( 127 sec) [ -18052.2684] [Topology ] . ( 130 sec) [ -18052.1893] [Topology ] . ( 134 sec) [ -18052.1479] [Topology ] . ( 137 sec) [ -18052.1256] [Topology ] . ( 140 sec) [ -18052.1134] [Topology ] . ( 143 sec) [ -18052.1068] [Topology ] . ( 143 sec) [ -18051.8995] [Alpha ][ 0.752531] . ( 143 sec) [ -18051.8995] [Topology ] . ( 147 sec) [ -18051.8650] [Topology ] . ( 150 sec) [ -18051.8479] [Topology ] . ( 153 sec) [ -18051.8387] [Topology ] . ( 156 sec) [ -18051.8336] [Topology ] . ( 159 sec) [ -18051.8308] [Topology ] . ( 162 sec) [ -18051.8293] [Topology ] . ( 162 sec) [ -18051.8225] [Alpha ][ 0.757306] . ( 163 sec) [ -18051.8225] [Topology ] . ( 166 sec) [ -18051.8200] [Topology ] . ( 169 sec) [ -18051.8186] [Topology ] . ( 172 sec) [ -18051.8179] [Topology ] . ( 172 sec) [ -18051.8177] [Alpha ][ 0.758160] . ( 173 sec) [ -18051.8177] [Topology ] . ( 176 sec) [ -18051.8171] [Topology ] . ( 176 sec) [ -18051.8171] [Alpha ][ 0.758160] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -18051.6319] [Topology ] . Checking for NNIs, optimizing five branches... . ( 226 sec) [ -18051.6167] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -18051.616684. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23069.4120] [Alpha ][ 0.500960] . ( 2 sec) [ -22755.9768] [ 3907] [depth= 10] . ( 2 sec) [ -22480.0998] [ 3847] [depth= 4] . ( 3 sec) [ -22057.5827] [ 3841] [depth= 2] . ( 3 sec) [ -21862.8233] [ 3799] [depth= 2] . ( 4 sec) [ -21600.5196] [ 3774] [depth= 2] . ( 4 sec) [ -21493.7689] [ 3766] [depth= 1] . ( 4 sec) [ -21477.1361] [ 3759] [depth= 1] . ( 5 sec) [ -21140.0901] [ 3690] [depth= 7] . ( 5 sec) [ -21132.3798] [ 3688] [depth= 1] . ( 6 sec) [ -20949.3561] [ 3683] [depth= 1] . ( 6 sec) [ -20745.7663] [ 3681] [depth= 1] . ( 7 sec) [ -20685.2942] [ 3680] [depth= 1] . ( 8 sec) [ -20546.6861] [ 3669] [depth= 3] . ( 8 sec) [ -20479.0775] [ 3639] [depth= 4] . ( 8 sec) [ -20323.0355] [ 3629] [depth= 2] . ( 9 sec) [ -20161.3162] [ 3604] [depth= 7] . ( 9 sec) [ -20150.5837] [ 3588] [depth= 1] . ( 10 sec) [ -20082.1052] [ 3581] [depth= 1] . ( 10 sec) [ -20080.8506] [ 3578] [depth= 1] . ( 11 sec) [ -19999.7244] [ 3559] [depth= 5] . ( 11 sec) [ -19983.1127] [ 3554] [depth= 1] . ( 12 sec) [ -19945.6374] [ 3536] [depth= 1] . ( 13 sec) [ -19809.0752] [ 3501] [depth= 3] . ( 13 sec) [ -19790.7806] [ 3493] [depth= 1] . ( 14 sec) [ -19784.3920] [ 3492] [depth= 1] . ( 15 sec) [ -19628.5708] [ 3438] [depth= 5] . ( 15 sec) [ -19327.0589] [ 3435] [depth= 1] . ( 15 sec) [ -19204.3301] [ 3430] [depth= 2] . ( 16 sec) [ -19085.1067] [ 3421] [depth= 1] . ( 17 sec) [ -19048.2780] [ 3417] [depth= 1] . ( 18 sec) [ -19009.6814] [ 3412] [depth= 1] . ( 18 sec) [ -18980.8987] [ 3403] [depth= 1] . ( 19 sec) [ -18924.3812] [ 3391] [depth= 1] . ( 20 sec) [ -18871.1690] [ 3395] [depth= 2] . ( 20 sec) [ -18858.5200] [ 3391] [depth= 4] . ( 21 sec) [ -18803.1232] [ 3387] [depth= 2] . ( 22 sec) [ -18779.1164] [ 3388] [depth= 1] . ( 23 sec) [ -18774.5224] [ 3391] [depth= 1] . ( 23 sec) [ -18672.6350] [ 3358] [depth= 7] . ( 25 sec) [ -18664.1470] [ 3365] [depth= 1] . ( 25 sec) [ -18661.7977] [ 3367] [depth= 1] . ( 26 sec) [ -18656.1662] [ 3368] [depth= 1] . ( 27 sec) [ -18650.5417] [ 3367] [depth= 1] . ( 28 sec) [ -18641.6499] [ 3362] [depth= 2] . ( 28 sec) [ -18634.2213] [ 3364] [depth= 2] . ( 29 sec) [ -18493.8191] [ 3354] [depth= 3] . ( 29 sec) [ -18453.2002] [ 3339] [depth= 4] . ( 30 sec) [ -18448.4221] [ 3336] [depth= 1] . ( 33 sec) [ -18386.2153] [ 3318] [depth= 1] . ( 34 sec) [ -18368.0124] [ 3308] [depth= 1] . ( 35 sec) [ -18260.8140] [Branch lengths ] . ( 36 sec) [ -18245.3993] [Alpha ][ 0.672666] . ( 37 sec) [ -18244.4956] [ 3313] [depth= 1] . ( 37 sec) [ -18152.4426] [ 3277] [depth= 6] . ( 40 sec) [ -18146.8299] [ 3278] [depth= 1] . ( 41 sec) [ -18144.9664] [ 3276] [depth= 1] . ( 42 sec) [ -18126.1096] [ 3272] [depth= 2] . ( 44 sec) [ -18124.4487] [ 3269] [depth= 1] . ( 45 sec) [ -18124.3075] [ 3270] [depth= 1] . ( 46 sec) [ -18098.9158] [ 3260] [depth= 2] . ( 49 sec) [ -18092.9807] [ 3260] [depth= 3] . ( 52 sec) [ -18091.2933] [ 3258] [depth= 1] . ( 53 sec) [ -18090.6020] [ 3260] [depth= 1] . ( 55 sec) [ -18089.2953] [ 3263] [depth= 1] . ( 59 sec) [ -18079.9185] [ 3261] [depth= 1] . ( 65 sec) [ -18058.4173] [Branch lengths ] . ( 66 sec) [ -18057.3201] [Alpha ][ 0.728969] . ( 80 sec) [ -18057.2879] [ 3265] [depth= 1] . ( 84 sec) [ -18056.3440] [ 3267] [depth= 1] . ( 109 sec) [ -18052.2454] [Branch lengths ] . ( 109 sec) [ -18052.1896] [Alpha ][ 0.742582] . ( 163 sec) [ -18051.7394] [Branch lengths ] . ( 163 sec) [ -18051.7394] [Topology ] . ( 166 sec) [ -18051.6799] [Topology ] . ( 169 sec) [ -18051.6569] [Topology ] . ( 172 sec) [ -18051.6447] [Topology ] . ( 175 sec) [ -18051.6379] [Topology ] . ( 178 sec) [ -18051.6342] [Topology ] . ( 181 sec) [ -18051.6321] [Topology ] . ( 182 sec) [ -18051.5775] [Alpha ][ 0.756187] . ( 182 sec) [ -18051.5775] [Topology ] . ( 185 sec) [ -18051.5682] [Topology ] . ( 188 sec) [ -18051.5635] [Topology ] . ( 192 sec) [ -18051.5609] [Topology ] . ( 195 sec) [ -18051.5595] [Topology ] . ( 198 sec) [ -18051.5587] [Topology ] . ( 198 sec) [ -18051.5574] [Alpha ][ 0.758288] . ( 199 sec) [ -18051.5574] [Topology ] . ( 202 sec) [ -18051.5564] [Topology ] . ( 202 sec) [ -18051.5564] [Alpha ][ 0.758288] . Checking for NNIs, optimizing five branches... . ( 227 sec) [ -18051.5488] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -18051.548791. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22889.0613] [Alpha ][ 0.500960] . ( 1 sec) [ -22653.0407] [ 3885] [depth= 3] . ( 2 sec) [ -22411.4904] [ 3839] [depth= 4] . ( 2 sec) [ -22279.0784] [ 3829] [depth= 3] . ( 3 sec) [ -22138.4364] [ 3816] [depth= 6] . ( 3 sec) [ -21945.3254] [ 3796] [depth= 5] . ( 4 sec) [ -21854.2296] [ 3786] [depth= 7] . ( 4 sec) [ -21709.3536] [ 3777] [depth= 3] . ( 5 sec) [ -21572.7298] [ 3768] [depth= 2] . ( 5 sec) [ -21527.5930] [ 3751] [depth= 1] . ( 5 sec) [ -21409.6305] [ 3754] [depth= 2] . ( 6 sec) [ -21221.6385] [ 3730] [depth= 4] . ( 7 sec) [ -21119.6767] [ 3696] [depth= 7] . ( 8 sec) [ -20977.8740] [ 3656] [depth= 4] . ( 8 sec) [ -20919.0387] [ 3653] [depth= 1] . ( 9 sec) [ -20764.7847] [ 3621] [depth= 4] . ( 9 sec) [ -20600.1324] [ 3635] [depth= 3] . ( 10 sec) [ -20595.1888] [ 3634] [depth= 1] . ( 10 sec) [ -20502.2534] [ 3603] [depth= 4] . ( 11 sec) [ -20428.7913] [ 3596] [depth= 1] . ( 12 sec) [ -20334.8219] [ 3558] [depth= 6] . ( 12 sec) [ -20311.4992] [ 3556] [depth= 1] . ( 13 sec) [ -20310.1416] [ 3556] [depth= 1] . ( 13 sec) [ -20303.6466] [ 3552] [depth= 1] . ( 14 sec) [ -20262.0270] [ 3553] [depth= 1] . ( 14 sec) [ -20245.9965] [ 3552] [depth= 1] . ( 15 sec) [ -20040.5476] [ 3525] [depth= 7] . ( 15 sec) [ -19982.3055] [ 3513] [depth= 1] . ( 16 sec) [ -19969.8895] [ 3505] [depth= 1] . ( 17 sec) [ -19958.3463] [ 3507] [depth= 1] . ( 18 sec) [ -19903.4394] [ 3508] [depth= 9] . ( 19 sec) [ -19889.7579] [ 3513] [depth= 2] . ( 19 sec) [ -19844.2280] [ 3502] [depth= 4] . ( 20 sec) [ -19717.0563] [ 3497] [depth= 6] . ( 20 sec) [ -19569.8117] [ 3467] [depth= 2] . ( 21 sec) [ -19566.4329] [ 3468] [depth= 3] . ( 21 sec) [ -19488.2851] [ 3453] [depth= 1] . ( 21 sec) [ -19359.2377] [ 3420] [depth= 8] . ( 22 sec) [ -19302.1790] [ 3410] [depth= 1] . ( 22 sec) [ -19295.3759] [ 3409] [depth= 1] . ( 23 sec) [ -19293.9795] [ 3410] [depth= 1] . ( 24 sec) [ -19253.1658] [ 3400] [depth= 1] . ( 24 sec) [ -19227.8845] [ 3388] [depth= 1] . ( 25 sec) [ -19222.4955] [ 3382] [depth= 1] . ( 27 sec) [ -19219.1656] [ 3382] [depth= 1] . ( 27 sec) [ -19044.8103] [ 3353] [depth= 2] . ( 28 sec) [ -18935.8098] [ 3343] [depth= 2] . ( 28 sec) [ -18809.5626] [ 3350] [depth= 2] . ( 29 sec) [ -18647.1747] [ 3299] [depth= 3] . ( 29 sec) [ -18644.3001] [ 3296] [depth= 1] . ( 29 sec) [ -18636.4782] [ 3302] [depth= 1] . ( 30 sec) [ -18570.3038] [ 3279] [depth= 3] . ( 31 sec) [ -18535.7475] [ 3278] [depth= 1] . ( 31 sec) [ -18511.3390] [ 3277] [depth= 1] . ( 33 sec) [ -18493.1773] [ 3277] [depth= 4] . ( 33 sec) [ -18238.7926] [ 3286] [depth= 1] . ( 34 sec) [ -18219.9923] [ 3277] [depth= 1] . ( 34 sec) [ -18215.3029] [ 3274] [depth= 1] . ( 36 sec) [ -18215.1024] [ 3277] [depth= 1] . ( 37 sec) [ -18149.8810] [Branch lengths ] . ( 37 sec) [ -18133.5923] [Alpha ][ 0.681808] . ( 38 sec) [ -18132.7590] [ 3274] [depth= 1] . ( 39 sec) [ -18128.9839] [ 3276] [depth= 3] . ( 39 sec) [ -18101.6480] [ 3266] [depth= 1] . ( 40 sec) [ -18099.9972] [ 3261] [depth= 2] . ( 42 sec) [ -18088.1679] [ 3263] [depth= 1] . ( 48 sec) [ -18086.7007] [ 3264] [depth= 3] . ( 49 sec) [ -18085.1122] [ 3257] [depth= 3] . ( 52 sec) [ -18082.2104] [ 3263] [depth= 1] . ( 52 sec) [ -18076.4380] [ 3257] [depth= 1] . ( 53 sec) [ -18073.9582] [ 3258] [depth= 1] . ( 63 sec) [ -18073.1960] [ 3263] [depth= 1] . ( 69 sec) [ -18060.6003] [Branch lengths ] . ( 69 sec) [ -18059.8856] [Alpha ][ 0.727330] . ( 72 sec) [ -18059.3970] [ 3257] [depth= 1] . ( 100 sec) [ -18057.1152] [Branch lengths ] . ( 101 sec) [ -18057.0398] [Alpha ][ 0.743071] . ( 133 sec) [ -18056.6455] [Branch lengths ] . ( 133 sec) [ -18056.6455] [Topology ] . ( 136 sec) [ -18056.4168] [Topology ] . ( 140 sec) [ -18056.1602] [Topology ] . ( 143 sec) [ -18056.1242] [Topology ] . ( 146 sec) [ -18056.1116] [Topology ] . ( 149 sec) [ -18056.1057] [Topology ] . ( 152 sec) [ -18056.1027] [Topology ] . ( 155 sec) [ -18056.1010] [Topology ] . ( 155 sec) [ -18056.0572] [Alpha ][ 0.755187] . ( 156 sec) [ -18056.0572] [Topology ] . ( 159 sec) [ -18056.0498] [Topology ] . ( 162 sec) [ -18056.0460] [Topology ] . ( 165 sec) [ -18056.0439] [Topology ] . ( 168 sec) [ -18056.0427] [Topology ] . ( 171 sec) [ -18056.0420] [Topology ] . ( 171 sec) [ -18056.0410] [Alpha ][ 0.757054] . ( 172 sec) [ -18056.0410] [Topology ] . ( 175 sec) [ -18056.0402] [Topology ] . ( 175 sec) [ -18056.0402] [Alpha ][ 0.757054] . Checking for NNIs, optimizing five branches... . ( 200 sec) [ -18055.8575] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -18055.857508. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22735.7415] [Alpha ][ 0.500960] . ( 2 sec) [ -22407.3249] [ 3889] [depth= 3] . ( 2 sec) [ -22181.5822] [ 3834] [depth= 8] . ( 3 sec) [ -22060.5780] [ 3831] [depth= 2] . ( 3 sec) [ -21881.7941] [ 3815] [depth= 6] . ( 4 sec) [ -21646.2764] [ 3773] [depth= 4] . ( 4 sec) [ -21398.4364] [ 3745] [depth= 5] . ( 5 sec) [ -21199.9748] [ 3714] [depth= 4] . ( 5 sec) [ -21134.0092] [ 3710] [depth= 1] . ( 6 sec) [ -20763.0568] [ 3639] [depth= 4] . ( 6 sec) [ -20573.8342] [ 3626] [depth= 9] . ( 7 sec) [ -20483.0230] [ 3615] [depth= 2] . ( 7 sec) [ -20440.7972] [ 3602] [depth= 1] . ( 8 sec) [ -20137.6249] [ 3601] [depth= 1] . ( 8 sec) [ -20116.8580] [ 3599] [depth= 2] . ( 9 sec) [ -19909.2727] [ 3592] [depth= 1] . ( 9 sec) [ -19881.3650] [ 3583] [depth= 4] . ( 10 sec) [ -19808.2457] [ 3564] [depth= 3] . ( 10 sec) [ -19741.5530] [ 3556] [depth= 1] . ( 11 sec) [ -19486.0209] [ 3543] [depth= 5] . ( 11 sec) [ -19482.2748] [ 3546] [depth= 1] . ( 12 sec) [ -19310.5091] [ 3508] [depth= 8] . ( 12 sec) [ -19292.3933] [ 3505] [depth= 1] . ( 13 sec) [ -19278.2551] [ 3505] [depth= 1] . ( 13 sec) [ -19128.8198] [ 3502] [depth= 1] . ( 14 sec) [ -19047.5940] [ 3467] [depth= 4] . ( 14 sec) [ -19043.8580] [ 3456] [depth= 3] . ( 15 sec) [ -19043.6380] [ 3461] [depth= 2] . ( 15 sec) [ -18821.2474] [ 3411] [depth= 4] . ( 16 sec) [ -18489.6078] [ 3321] [depth= 5] . ( 17 sec) [ -18478.9410] [ 3317] [depth= 2] . ( 18 sec) [ -18459.1527] [ 3314] [depth= 1] . ( 18 sec) [ -18417.2975] [ 3312] [depth= 3] . ( 19 sec) [ -18392.4317] [ 3309] [depth= 3] . ( 20 sec) [ -18369.8706] [ 3307] [depth= 1] . ( 20 sec) [ -18327.4077] [ 3291] [depth= 1] . ( 21 sec) [ -18323.3535] [ 3284] [depth= 3] . ( 21 sec) [ -18312.1281] [ 3287] [depth= 6] . ( 22 sec) [ -18260.5718] [ 3271] [depth= 1] . ( 24 sec) [ -18191.5185] [ 3264] [depth= 3] . ( 28 sec) [ -18187.5137] [ 3265] [depth= 1] . ( 30 sec) [ -18165.3325] [ 3264] [depth= 1] . ( 30 sec) [ -18153.7793] [ 3265] [depth= 1] . ( 31 sec) [ -18149.7076] [ 3262] [depth= 1] . ( 33 sec) [ -18127.8328] [ 3261] [depth= 1] . ( 34 sec) [ -18083.0939] [Branch lengths ] . ( 34 sec) [ -18069.6744] [Alpha ][ 0.664199] . ( 39 sec) [ -18067.2462] [ 3267] [depth= 3] . ( 45 sec) [ -18066.9904] [ 3268] [depth= 1] . ( 86 sec) [ -18057.8421] [Branch lengths ] . ( 87 sec) [ -18057.1029] [Alpha ][ 0.709746] . ( 142 sec) [ -18054.7683] [Branch lengths ] . ( 143 sec) [ -18054.7683] [Topology ] . ( 146 sec) [ -18054.4404] [Topology ] . ( 149 sec) [ -18054.3229] [Topology ] . ( 152 sec) [ -18054.2633] [Topology ] . ( 155 sec) [ -18054.2320] [Topology ] . ( 158 sec) [ -18054.2154] [Topology ] . ( 161 sec) [ -18054.2065] [Topology ] . ( 161 sec) [ -18053.8047] [Alpha ][ 0.744800] . ( 162 sec) [ -18053.8047] [Topology ] . ( 165 sec) [ -18053.7419] [Topology ] . ( 168 sec) [ -18053.7119] [Topology ] . ( 171 sec) [ -18053.6961] [Topology ] . ( 174 sec) [ -18053.6877] [Topology ] . ( 177 sec) [ -18053.6831] [Topology ] . ( 180 sec) [ -18053.6807] [Topology ] . ( 181 sec) [ -18053.6658] [Alpha ][ 0.751856] . ( 181 sec) [ -18053.6658] [Topology ] . ( 184 sec) [ -18053.6610] [Topology ] . ( 187 sec) [ -18053.6586] [Topology ] . ( 190 sec) [ -18053.6572] [Topology ] . ( 193 sec) [ -18053.6565] [Topology ] . ( 193 sec) [ -18053.6559] [Alpha ][ 0.753279] . ( 194 sec) [ -18053.6559] [Topology ] . ( 197 sec) [ -18053.6552] [Topology ] . ( 197 sec) [ -18053.6552] [Alpha ][ 0.753279] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -18053.655182. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -18178.5487] [Alpha ][ 0.611907] . ( 1 sec) [ -18178.5487] [Topology ] . ( 4 sec) [ -18078.2315] [Topology ] . ( 7 sec) [ -18069.5546] [Topology ] . ( 10 sec) [ -18067.9397] [Topology ] . ( 13 sec) [ -18067.8156] [Topology ] . ( 16 sec) [ -18067.4540] [Topology ] . ( 20 sec) [ -18067.6241] [Topology ] . Moving backward . ( 20 sec) [ -18066.7104] [Topology ] . ( 23 sec) [ -18066.3550] [Topology ] . ( 26 sec) [ -18066.3089] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -18061.5099] [Alpha ][ 0.723516] . ( 54 sec) [ -18061.5099] [Topology ] . ( 57 sec) [ -18060.8363] [Topology ] . ( 60 sec) [ -18060.5480] [Topology ] . ( 63 sec) [ -18060.4022] [Topology ] . ( 66 sec) [ -18060.3259] [Topology ] . ( 70 sec) [ -18060.2846] [Topology ] . ( 73 sec) [ -18060.2625] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -18060.0867] [Alpha ][ 0.746673] . ( 98 sec) [ -18060.0867] [Topology ] . ( 101 sec) [ -18060.0368] [Topology ] . ( 104 sec) [ -18060.0115] [Topology ] . ( 107 sec) [ -18059.9979] [Topology ] . ( 110 sec) [ -18059.9904] [Topology ] . ( 113 sec) [ -18059.9863] [Topology ] . ( 116 sec) [ -18059.9841] [Topology ] . Checking for NNIs, optimizing five branches... . ( 141 sec) [ -18059.9715] [Alpha ][ 0.753168] . ( 142 sec) [ -18059.9715] [Topology ] . ( 145 sec) [ -18059.9673] [Topology ] . ( 148 sec) [ -18059.9651] [Topology ] . ( 151 sec) [ -18059.9639] [Topology ] . ( 154 sec) [ -18059.9633] [Topology ] . Checking for NNIs, optimizing five branches... . ( 179 sec) [ -18059.9627] [Alpha ][ 0.754490] . ( 179 sec) [ -18059.9627] [Topology ] . ( 182 sec) [ -18059.9621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 207 sec) [ -18059.9621] [Alpha ][ 0.754490] . ( 208 sec) [ -18059.9621] [Topology ] . ( 211 sec) [ -18059.9617] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 261 sec) [ -18178.5487] [Alpha ][ 0.611907] . ( 262 sec) [ -18176.6899] [ 3274] [depth= 1] . ( 263 sec) [ -18176.2365] [ 3272] [depth= 1] . ( 264 sec) [ -18173.3351] [ 3274] [depth= 1] . ( 268 sec) [ -18169.5680] [ 3279] [depth= 1] . ( 270 sec) [ -18168.0103] [ 3274] [depth= 1] . ( 276 sec) [ -18163.4481] [ 3273] [depth= 1] . ( 276 sec) [ -18163.3021] [ 3273] [depth= 1] . ( 277 sec) [ -18161.4043] [ 3274] [depth= 1] . ( 277 sec) [ -18158.7458] [ 3273] [depth= 1] . ( 279 sec) [ -18151.5756] [ 3273] [depth= 2] . ( 281 sec) [ -18135.4753] [ 3269] [depth= 2] . ( 282 sec) [ -18133.6824] [ 3272] [depth= 1] . ( 283 sec) [ -18131.0336] [ 3267] [depth= 2] . ( 283 sec) [ -18125.8354] [ 3268] [depth= 1] . ( 284 sec) [ -18118.3604] [ 3263] [depth= 3] . ( 284 sec) [ -18113.1297] [ 3260] [depth= 1] . ( 288 sec) [ -18111.3813] [ 3264] [depth= 1] . ( 288 sec) [ -18105.5944] [ 3260] [depth= 3] . ( 289 sec) [ -18103.9480] [ 3260] [depth= 1] . ( 292 sec) [ -18102.8742] [ 3260] [depth= 1] . ( 294 sec) [ -18070.0648] [Branch lengths ] . ( 295 sec) [ -18066.2468] [Alpha ][ 0.711148] . ( 302 sec) [ -18063.1961] [ 3261] [depth= 2] . ( 308 sec) [ -18062.6789] [ 3262] [depth= 1] . ( 316 sec) [ -18061.8072] [ 3261] [depth= 1] . ( 327 sec) [ -18058.2511] [Branch lengths ] . ( 328 sec) [ -18058.0679] [Alpha ][ 0.734464] . ( 362 sec) [ -18057.3162] [Branch lengths ] . ( 362 sec) [ -18057.3162] [Topology ] . ( 365 sec) [ -18057.2145] [Topology ] . ( 368 sec) [ -18057.1762] [Topology ] . ( 371 sec) [ -18057.1555] [Topology ] . ( 374 sec) [ -18057.1440] [Topology ] . ( 377 sec) [ -18057.1376] [Topology ] . ( 380 sec) [ -18057.1339] [Topology ] . ( 381 sec) [ -18057.0207] [Alpha ][ 0.753094] . ( 381 sec) [ -18057.0207] [Topology ] . ( 384 sec) [ -18057.0029] [Topology ] . ( 387 sec) [ -18056.9939] [Topology ] . ( 390 sec) [ -18056.9889] [Topology ] . ( 393 sec) [ -18056.9861] [Topology ] . ( 396 sec) [ -18056.9845] [Topology ] . ( 399 sec) [ -18056.9836] [Topology ] . ( 400 sec) [ -18056.9790] [Alpha ][ 0.757039] . ( 400 sec) [ -18056.9790] [Topology ] . ( 403 sec) [ -18056.9774] [Topology ] . ( 406 sec) [ -18056.9765] [Topology ] . ( 407 sec) [ -18056.9765] [Alpha ][ 0.757796] . ( 407 sec) [ -18056.9765] [Topology ] . ( 410 sec) [ -18056.9758] [Topology ] . ( 411 sec) [ -18056.9758] [Alpha ][ 0.757796] . Checking for NNIs, optimizing five branches... . ( 436 sec) [ -18056.6146] [Topology ] . Checking for NNIs, optimizing five branches... . ( 463 sec) [ -18056.1621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 490 sec) [ -18056.0649] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -18059.961750 . Log likelihood obtained after SPR moves : -18056.064925 . Log likelihood of the current tree: -18056.064925. . Printing the most likely tree in file 'proteic_M2479_30x627_2005.phy_phyml_tree.txt'... . Best log likelihood : -18051.548791 . Time used 0h8m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1698.84user 0.00system 28:29.90elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps