.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1504_37x547_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... . 429 patterns found. (out of a total of 547 sites) . 136 sites without polymorphism (24.86%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22165.6535] [Alpha ][ 0.500960] . ( 2 sec) [ -21850.1454] [ 3741] [depth= 12] . ( 2 sec) [ -21583.8092] [ 3763] [depth= 12] . ( 3 sec) [ -21343.9979] [ 3721] [depth= 1] . ( 3 sec) [ -21217.6373] [ 3705] [depth= 9] . ( 3 sec) [ -21195.9172] [ 3697] [depth= 1] . ( 4 sec) [ -21044.5294] [ 3680] [depth= 10] . ( 4 sec) [ -20964.6171] [ 3674] [depth= 1] . ( 5 sec) [ -20932.2573] [ 3671] [depth= 2] . ( 6 sec) [ -20757.8281] [ 3627] [depth= 1] . ( 6 sec) [ -20747.9362] [ 3620] [depth= 1] . ( 7 sec) [ -20591.6391] [ 3593] [depth= 3] . ( 7 sec) [ -20434.5436] [ 3598] [depth= 2] . ( 8 sec) [ -20063.3300] [ 3542] [depth= 9] . ( 8 sec) [ -20061.8767] [ 3547] [depth= 2] . ( 8 sec) [ -19849.2083] [ 3491] [depth= 11] . ( 9 sec) [ -19635.5849] [ 3461] [depth= 13] . ( 10 sec) [ -19417.3248] [ 3414] [depth= 3] . ( 10 sec) [ -19093.0221] [ 3336] [depth= 10] . ( 11 sec) [ -19074.5447] [ 3321] [depth= 1] . ( 11 sec) [ -18781.2597] [ 3252] [depth= 6] . ( 12 sec) [ -18362.6812] [ 3182] [depth= 1] . ( 12 sec) [ -17881.5527] [ 3146] [depth= 9] . ( 13 sec) [ -17533.8737] [ 3045] [depth= 8] . ( 13 sec) [ -17402.3171] [ 2995] [depth= 3] . ( 14 sec) [ -17329.4233] [ 2990] [depth= 2] . ( 14 sec) [ -17153.7889] [ 2941] [depth= 3] . ( 15 sec) [ -16923.6062] [ 2937] [depth= 3] . ( 15 sec) [ -16747.2675] [ 2902] [depth= 7] . ( 15 sec) [ -16722.1104] [ 2902] [depth= 2] . ( 16 sec) [ -16361.7065] [ 2845] [depth= 7] . ( 17 sec) [ -16247.0546] [ 2806] [depth= 1] . ( 17 sec) [ -16213.2616] [ 2792] [depth= 1] . ( 18 sec) [ -16190.8113] [ 2797] [depth= 1] . ( 19 sec) [ -16174.7866] [ 2792] [depth= 1] . ( 19 sec) [ -16059.7659] [ 2752] [depth= 2] . ( 20 sec) [ -15854.0162] [ 2713] [depth= 8] . ( 20 sec) [ -15839.2239] [ 2706] [depth= 11] . ( 21 sec) [ -15799.5250] [ 2696] [depth= 4] . ( 21 sec) [ -15747.6388] [ 2686] [depth= 1] . ( 22 sec) [ -15490.5637] [ 2609] [depth= 8] . ( 22 sec) [ -15477.8361] [ 2608] [depth= 1] . ( 23 sec) [ -15426.1190] [ 2603] [depth= 2] . ( 23 sec) [ -15347.2741] [ 2586] [depth= 3] . ( 24 sec) [ -15281.7598] [ 2548] [depth= 3] . ( 24 sec) [ -15142.8661] [ 2515] [depth= 2] . ( 25 sec) [ -14983.1899] [ 2509] [depth= 2] . ( 25 sec) [ -14979.5194] [ 2524] [depth= 9] . ( 26 sec) [ -14769.2202] [ 2493] [depth= 2] . ( 27 sec) [ -14548.5213] [ 2467] [depth= 6] . ( 27 sec) [ -14301.5898] [ 2415] [depth= 6] . ( 28 sec) [ -14140.0709] [ 2367] [depth= 5] . ( 28 sec) [ -14094.2707] [ 2366] [depth= 3] . ( 29 sec) [ -13989.4700] [ 2342] [depth= 1] . ( 29 sec) [ -13972.7720] [ 2344] [depth= 1] . ( 30 sec) [ -13966.8940] [ 2342] [depth= 1] . ( 31 sec) [ -13804.6760] [ 2298] [depth= 1] . ( 32 sec) [ -13420.1446] [ 2239] [depth= 7] . ( 33 sec) [ -13410.3651] [ 2225] [depth= 3] . ( 34 sec) [ -13324.3617] [ 2205] [depth= 1] . ( 34 sec) [ -13220.5813] [ 2187] [depth= 1] . ( 35 sec) [ -12999.1427] [ 2153] [depth= 2] . ( 35 sec) [ -12983.7102] [ 2148] [depth= 3] . ( 36 sec) [ -12969.5939] [ 2142] [depth= 1] . ( 37 sec) [ -12966.4483] [ 2143] [depth= 1] . ( 38 sec) [ -12914.0251] [ 2136] [depth= 2] . ( 39 sec) [ -12895.0103] [ 2140] [depth= 1] . ( 39 sec) [ -12833.0812] [ 2112] [depth= 3] . ( 40 sec) [ -12830.8535] [ 2116] [depth= 3] . ( 41 sec) [ -12796.1408] [ 2097] [depth= 1] . ( 41 sec) [ -12791.5952] [ 2096] [depth= 1] . ( 42 sec) [ -12789.7434] [ 2096] [depth= 2] . ( 43 sec) [ -12699.8682] [Branch lengths ] . ( 44 sec) [ -12685.3831] [Alpha ][ 0.710151] . ( 45 sec) [ -12674.6231] [ 2093] [depth= 1] . ( 46 sec) [ -12667.6893] [ 2094] [depth= 1] . ( 46 sec) [ -12627.9935] [ 2080] [depth= 1] . ( 48 sec) [ -12627.1665] [ 2079] [depth= 1] . ( 48 sec) [ -12626.1439] [ 2076] [depth= 2] . ( 53 sec) [ -12624.9607] [ 2073] [depth= 1] . ( 58 sec) [ -12619.4167] [ 2071] [depth= 1] . ( 61 sec) [ -12614.7517] [ 2071] [depth= 2] . ( 72 sec) [ -12613.9484] [ 2071] [depth= 2] . ( 74 sec) [ -12610.8977] [ 2078] [depth= 1] . ( 78 sec) [ -12597.0784] [Branch lengths ] . ( 79 sec) [ -12596.7162] [Alpha ][ 0.751593] . ( 84 sec) [ -12595.3159] [ 2075] [depth= 1] . ( 96 sec) [ -12593.7460] [ 2070] [depth= 1] . ( 101 sec) [ -12593.6310] [ 2069] [depth= 1] . ( 107 sec) [ -12593.4087] [ 2071] [depth= 1] . ( 114 sec) [ -12593.0920] [ 2072] [depth= 2] . ( 119 sec) [ -12586.7512] [Branch lengths ] . ( 120 sec) [ -12586.6616] [Alpha ][ 0.772843] . ( 163 sec) [ -12586.1423] [Branch lengths ] . ( 163 sec) [ -12586.1423] [Topology ] . ( 167 sec) [ -12586.0023] [Topology ] . ( 171 sec) [ -12585.6569] [Topology ] . ( 175 sec) [ -12585.6076] [Topology ] . ( 178 sec) [ -12585.5929] [Topology ] . ( 182 sec) [ -12585.5863] [Topology ] . ( 186 sec) [ -12585.5828] [Topology ] . ( 189 sec) [ -12585.5807] [Topology ] . ( 190 sec) [ -12585.5440] [Alpha ][ 0.787198] . ( 190 sec) [ -12585.5440] [Topology ] . ( 194 sec) [ -12585.5400] [Topology ] . ( 198 sec) [ -12585.5377] [Topology ] . ( 201 sec) [ -12585.5362] [Topology ] . ( 205 sec) [ -12585.5353] [Topology ] . ( 206 sec) [ -12585.5352] [Alpha ][ 0.787985] . ( 206 sec) [ -12585.5352] [Topology ] . ( 210 sec) [ -12585.5346] [Topology ] . ( 210 sec) [ -12585.5346] [Alpha ][ 0.787985] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12585.534595. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22763.3624] [Alpha ][ 0.500960] . ( 2 sec) [ -22388.4060] [ 3639] [depth= 14] . ( 2 sec) [ -22299.8514] [ 3632] [depth= 1] . ( 3 sec) [ -22021.8652] [ 3572] [depth= 7] . ( 3 sec) [ -21796.5622] [ 3512] [depth= 1] . ( 4 sec) [ -20651.8302] [ 3447] [depth= 5] . ( 4 sec) [ -20599.8544] [ 3467] [depth= 1] . ( 4 sec) [ -20349.9650] [ 3438] [depth= 5] . ( 5 sec) [ -20340.6776] [ 3436] [depth= 2] . ( 5 sec) [ -20174.4488] [ 3423] [depth= 6] . ( 6 sec) [ -20092.8639] [ 3413] [depth= 1] . ( 6 sec) [ -19958.5532] [ 3376] [depth= 2] . ( 6 sec) [ -19934.2585] [ 3375] [depth= 1] . ( 7 sec) [ -19777.5576] [ 3363] [depth= 5] . ( 8 sec) [ -19716.2143] [ 3362] [depth= 1] . ( 8 sec) [ -19529.2988] [ 3327] [depth= 1] . ( 9 sec) [ -19264.8059] [ 3269] [depth= 7] . ( 9 sec) [ -19182.3835] [ 3269] [depth= 1] . ( 10 sec) [ -18593.3753] [ 3141] [depth= 5] . ( 10 sec) [ -18581.9945] [ 3135] [depth= 1] . ( 10 sec) [ -18421.4113] [ 3094] [depth= 1] . ( 11 sec) [ -18228.5410] [ 3077] [depth= 3] . ( 11 sec) [ -18047.9588] [ 3055] [depth= 5] . ( 12 sec) [ -17609.9198] [ 3008] [depth= 1] . ( 12 sec) [ -17573.2459] [ 2995] [depth= 11] . ( 13 sec) [ -17471.7007] [ 2987] [depth= 2] . ( 13 sec) [ -17374.4824] [ 2979] [depth= 1] . ( 14 sec) [ -17213.2484] [ 2929] [depth= 1] . ( 14 sec) [ -17190.0953] [ 2918] [depth= 4] . ( 15 sec) [ -17103.4537] [ 2913] [depth= 1] . ( 15 sec) [ -17038.6871] [ 2878] [depth= 6] . ( 16 sec) [ -17034.7645] [ 2882] [depth= 2] . ( 16 sec) [ -16778.5604] [ 2823] [depth= 5] . ( 17 sec) [ -16697.5338] [ 2802] [depth= 5] . ( 17 sec) [ -16396.5760] [ 2794] [depth= 1] . ( 18 sec) [ -16287.4031] [ 2755] [depth= 3] . ( 18 sec) [ -16165.0008] [ 2711] [depth= 8] . ( 19 sec) [ -15860.6017] [ 2672] [depth= 7] . ( 19 sec) [ -15545.2824] [ 2674] [depth= 1] . ( 20 sec) [ -15533.7854] [ 2642] [depth= 4] . ( 20 sec) [ -15065.3077] [ 2558] [depth= 10] . ( 21 sec) [ -15008.9824] [ 2545] [depth= 1] . ( 21 sec) [ -14640.5355] [ 2506] [depth= 1] . ( 22 sec) [ -14358.4326] [ 2434] [depth= 7] . ( 22 sec) [ -14355.4823] [ 2433] [depth= 1] . ( 23 sec) [ -14334.5137] [ 2439] [depth= 7] . ( 23 sec) [ -14309.6811] [ 2442] [depth= 1] . ( 24 sec) [ -13966.8631] [ 2357] [depth= 5] . ( 24 sec) [ -13853.5665] [ 2332] [depth= 1] . ( 25 sec) [ -13733.2378] [ 2312] [depth= 2] . ( 25 sec) [ -13701.1896] [ 2301] [depth= 1] . ( 27 sec) [ -13602.7490] [ 2308] [depth= 2] . ( 27 sec) [ -13539.4950] [ 2273] [depth= 4] . ( 28 sec) [ -13472.2049] [ 2251] [depth= 1] . ( 28 sec) [ -13457.3641] [ 2253] [depth= 1] . ( 29 sec) [ -13451.0653] [ 2251] [depth= 1] . ( 30 sec) [ -13342.6047] [ 2226] [depth= 6] . ( 30 sec) [ -13322.3000] [ 2244] [depth= 1] . ( 31 sec) [ -13314.5445] [ 2241] [depth= 1] . ( 32 sec) [ -13279.7799] [ 2219] [depth= 2] . ( 32 sec) [ -13198.4159] [ 2195] [depth= 1] . ( 33 sec) [ -13178.6415] [ 2187] [depth= 2] . ( 34 sec) [ -13145.1449] [ 2170] [depth= 1] . ( 34 sec) [ -13054.9866] [ 2138] [depth= 1] . ( 36 sec) [ -12985.7835] [ 2131] [depth= 3] . ( 37 sec) [ -12978.6643] [ 2128] [depth= 2] . ( 38 sec) [ -12844.5818] [ 2097] [depth= 2] . ( 39 sec) [ -12841.8241] [ 2100] [depth= 1] . ( 39 sec) [ -12825.7593] [ 2094] [depth= 2] . ( 41 sec) [ -12694.9912] [Branch lengths ] . ( 42 sec) [ -12674.5973] [Alpha ][ 0.753355] . ( 44 sec) [ -12668.9915] [ 2091] [depth= 1] . ( 47 sec) [ -12623.6391] [ 2082] [depth= 3] . ( 50 sec) [ -12617.5035] [ 2077] [depth= 1] . ( 51 sec) [ -12616.7831] [ 2077] [depth= 1] . ( 54 sec) [ -12604.3700] [ 2069] [depth= 1] . ( 59 sec) [ -12603.8932] [ 2071] [depth= 1] . ( 61 sec) [ -12599.8068] [ 2073] [depth= 2] . ( 64 sec) [ -12598.5173] [ 2073] [depth= 1] . ( 64 sec) [ -12597.7337] [ 2069] [depth= 3] . ( 65 sec) [ -12597.6591] [ 2069] [depth= 1] . ( 68 sec) [ -12595.7453] [ 2064] [depth= 1] . ( 75 sec) [ -12594.9582] [ 2064] [depth= 1] . ( 77 sec) [ -12588.5164] [Branch lengths ] . ( 77 sec) [ -12588.4228] [Alpha ][ 0.775101] . ( 89 sec) [ -12587.8869] [ 2068] [depth= 1] . ( 90 sec) [ -12587.6979] [ 2069] [depth= 2] . ( 113 sec) [ -12585.6998] [Branch lengths ] . ( 114 sec) [ -12585.6869] [Alpha ][ 0.783578] . ( 152 sec) [ -12585.5719] [Branch lengths ] . ( 152 sec) [ -12585.5719] [Topology ] . ( 156 sec) [ -12585.5558] [Topology ] . ( 159 sec) [ -12585.5488] [Topology ] . ( 163 sec) [ -12585.5446] [Topology ] . ( 167 sec) [ -12585.5420] [Topology ] . ( 170 sec) [ -12585.5404] [Topology ] . ( 174 sec) [ -12585.5394] [Topology ] . ( 175 sec) [ -12585.5363] [Alpha ][ 0.787723] . ( 175 sec) [ -12585.5363] [Topology ] . ( 179 sec) [ -12585.5353] [Topology ] . ( 182 sec) [ -12585.5346] [Topology ] . ( 183 sec) [ -12585.5346] [Alpha ][ 0.787723] . ( 183 sec) [ -12585.5346] [Topology ] . ( 187 sec) [ -12585.5342] [Topology ] . ( 187 sec) [ -12585.5342] [Alpha ][ 0.787723] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12585.534248. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -21880.2288] [Alpha ][ 0.500960] . ( 2 sec) [ -21348.1117] [ 3701] [depth= 10] . ( 3 sec) [ -20849.8046] [ 3609] [depth= 11] . ( 3 sec) [ -20657.6362] [ 3591] [depth= 1] . ( 4 sec) [ -20580.3382] [ 3581] [depth= 2] . ( 4 sec) [ -20433.9790] [ 3543] [depth= 1] . ( 4 sec) [ -20250.8124] [ 3526] [depth= 7] . ( 5 sec) [ -19999.6780] [ 3484] [depth= 3] . ( 5 sec) [ -19700.1325] [ 3396] [depth= 1] . ( 6 sec) [ -19483.7060] [ 3371] [depth= 4] . ( 6 sec) [ -19313.0795] [ 3345] [depth= 5] . ( 7 sec) [ -19253.0511] [ 3332] [depth= 4] . ( 7 sec) [ -19200.8020] [ 3317] [depth= 1] . ( 7 sec) [ -19174.2890] [ 3304] [depth= 13] . ( 8 sec) [ -19118.7087] [ 3324] [depth= 1] . ( 8 sec) [ -18881.7229] [ 3283] [depth= 6] . ( 9 sec) [ -18644.4974] [ 3225] [depth= 9] . ( 10 sec) [ -18523.3391] [ 3204] [depth= 1] . ( 10 sec) [ -18211.6595] [ 3144] [depth= 1] . ( 10 sec) [ -18077.0408] [ 3119] [depth= 5] . ( 11 sec) [ -17572.6327] [ 3011] [depth= 8] . ( 11 sec) [ -17501.8688] [ 3009] [depth= 1] . ( 12 sec) [ -17318.2362] [ 3013] [depth= 7] . ( 12 sec) [ -17219.1480] [ 3022] [depth= 7] . ( 13 sec) [ -17196.8520] [ 3017] [depth= 1] . ( 13 sec) [ -16889.2031] [ 2914] [depth= 9] . ( 14 sec) [ -16882.5414] [ 2914] [depth= 1] . ( 14 sec) [ -16858.8232] [ 2932] [depth= 1] . ( 14 sec) [ -16712.5707] [ 2879] [depth= 2] . ( 15 sec) [ -16580.8862] [ 2847] [depth= 5] . ( 16 sec) [ -16265.0533] [ 2791] [depth= 2] . ( 16 sec) [ -16205.6467] [ 2783] [depth= 1] . ( 16 sec) [ -15842.9075] [ 2775] [depth= 2] . ( 17 sec) [ -15454.0096] [ 2670] [depth= 8] . ( 18 sec) [ -15430.1897] [ 2667] [depth= 1] . ( 18 sec) [ -15205.7177] [ 2615] [depth= 7] . ( 19 sec) [ -15012.6420] [ 2563] [depth= 3] . ( 19 sec) [ -14882.1668] [ 2532] [depth= 6] . ( 20 sec) [ -14799.9440] [ 2505] [depth= 1] . ( 20 sec) [ -14783.9357] [ 2500] [depth= 2] . ( 21 sec) [ -14732.0474] [ 2498] [depth= 2] . ( 21 sec) [ -14653.8603] [ 2487] [depth= 3] . ( 22 sec) [ -14555.7272] [ 2476] [depth= 3] . ( 22 sec) [ -14497.3338] [ 2470] [depth= 2] . ( 23 sec) [ -14389.4315] [ 2454] [depth= 8] . ( 23 sec) [ -14380.2798] [ 2451] [depth= 3] . ( 24 sec) [ -14374.8145] [ 2446] [depth= 2] . ( 24 sec) [ -14311.4063] [ 2436] [depth= 4] . ( 25 sec) [ -14287.4696] [ 2435] [depth= 1] . ( 25 sec) [ -14183.0531] [ 2414] [depth= 8] . ( 26 sec) [ -14107.3735] [ 2391] [depth= 5] . ( 26 sec) [ -14094.9977] [ 2389] [depth= 1] . ( 27 sec) [ -14023.0919] [ 2373] [depth= 2] . ( 27 sec) [ -14010.7839] [ 2396] [depth= 1] . ( 28 sec) [ -14009.7201] [ 2393] [depth= 3] . ( 28 sec) [ -14004.3519] [ 2390] [depth= 2] . ( 29 sec) [ -13892.9571] [ 2357] [depth= 1] . ( 29 sec) [ -13824.4430] [ 2330] [depth= 1] . ( 29 sec) [ -13750.0881] [ 2306] [depth= 3] . ( 30 sec) [ -13748.8542] [ 2307] [depth= 1] . ( 31 sec) [ -13736.4672] [ 2316] [depth= 1] . ( 31 sec) [ -13693.1119] [ 2308] [depth= 1] . ( 32 sec) [ -13559.8886] [ 2311] [depth= 3] . ( 32 sec) [ -13524.5810] [ 2296] [depth= 2] . ( 33 sec) [ -13516.9904] [ 2293] [depth= 1] . ( 34 sec) [ -13499.6607] [ 2294] [depth= 5] . ( 34 sec) [ -13430.6378] [ 2277] [depth= 1] . ( 35 sec) [ -13303.6393] [ 2253] [depth= 1] . ( 35 sec) [ -13282.7744] [ 2244] [depth= 1] . ( 36 sec) [ -13242.2263] [ 2234] [depth= 3] . ( 38 sec) [ -13211.5350] [ 2221] [depth= 1] . ( 38 sec) [ -13202.9371] [ 2222] [depth= 1] . ( 38 sec) [ -12929.7867] [ 2138] [depth= 1] . ( 39 sec) [ -12911.5166] [ 2135] [depth= 1] . ( 40 sec) [ -12831.9550] [ 2107] [depth= 1] . ( 42 sec) [ -12714.2305] [Branch lengths ] . ( 43 sec) [ -12693.5875] [Alpha ][ 0.754404] . ( 44 sec) [ -12690.0930] [ 2096] [depth= 1] . ( 49 sec) [ -12684.3268] [ 2094] [depth= 1] . ( 50 sec) [ -12642.7067] [ 2085] [depth= 1] . ( 50 sec) [ -12637.1709] [ 2083] [depth= 1] . ( 52 sec) [ -12626.7574] [ 2080] [depth= 1] . ( 53 sec) [ -12609.6170] [ 2074] [depth= 2] . ( 54 sec) [ -12596.8920] [ 2068] [depth= 1] . ( 55 sec) [ -12595.8730] [ 2067] [depth= 2] . ( 59 sec) [ -12595.0456] [ 2072] [depth= 1] . ( 83 sec) [ -12586.5238] [Branch lengths ] . ( 84 sec) [ -12586.4211] [Alpha ][ 0.777287] . ( 97 sec) [ -12586.3992] [ 2069] [depth= 1] . ( 121 sec) [ -12585.6903] [Branch lengths ] . ( 122 sec) [ -12585.6840] [Alpha ][ 0.783229] . ( 122 sec) [ -12585.6840] [Topology ] . ( 126 sec) [ -12585.6113] [Topology ] . ( 130 sec) [ -12585.5823] [Topology ] . ( 133 sec) [ -12585.5654] [Topology ] . ( 137 sec) [ -12585.5551] [Topology ] . ( 141 sec) [ -12585.5488] [Topology ] . ( 144 sec) [ -12585.5449] [Topology ] . ( 145 sec) [ -12585.5422] [Alpha ][ 0.787104] . ( 145 sec) [ -12585.5422] [Topology ] . ( 149 sec) [ -12585.5390] [Topology ] . ( 153 sec) [ -12585.5371] [Topology ] . ( 156 sec) [ -12585.5359] [Topology ] . ( 160 sec) [ -12585.5351] [Topology ] . ( 161 sec) [ -12585.5350] [Alpha ][ 0.787892] . ( 161 sec) [ -12585.5350] [Topology ] . ( 164 sec) [ -12585.5345] [Topology ] . ( 165 sec) [ -12585.5345] [Alpha ][ 0.787892] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12585.534478. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22112.8374] [Alpha ][ 0.500960] . ( 1 sec) [ -21842.7856] [ 3747] [depth= 4] . ( 2 sec) [ -21289.4682] [ 3718] [depth= 9] . ( 2 sec) [ -21278.4120] [ 3717] [depth= 1] . ( 3 sec) [ -21197.1186] [ 3705] [depth= 4] . ( 3 sec) [ -21131.1223] [ 3676] [depth= 2] . ( 4 sec) [ -21016.4204] [ 3664] [depth= 4] . ( 4 sec) [ -21007.3649] [ 3654] [depth= 4] . ( 4 sec) [ -20665.4540] [ 3652] [depth= 9] . ( 5 sec) [ -20579.4313] [ 3622] [depth= 2] . ( 5 sec) [ -20295.2899] [ 3547] [depth= 3] . ( 6 sec) [ -20184.5956] [ 3529] [depth= 1] . ( 6 sec) [ -20127.9185] [ 3520] [depth= 1] . ( 7 sec) [ -19934.4067] [ 3467] [depth= 9] . ( 7 sec) [ -19875.3832] [ 3468] [depth= 3] . ( 7 sec) [ -19775.2762] [ 3452] [depth= 1] . ( 8 sec) [ -19606.9870] [ 3423] [depth= 7] . ( 8 sec) [ -19545.1961] [ 3406] [depth= 1] . ( 9 sec) [ -19517.8266] [ 3392] [depth= 1] . ( 9 sec) [ -19420.3599] [ 3387] [depth= 1] . ( 10 sec) [ -19321.1644] [ 3367] [depth= 5] . ( 10 sec) [ -19155.9548] [ 3305] [depth= 5] . ( 11 sec) [ -18755.0606] [ 3250] [depth= 1] . ( 11 sec) [ -18473.9494] [ 3189] [depth= 15] . ( 12 sec) [ -18098.4098] [ 3134] [depth= 1] . ( 12 sec) [ -17995.6091] [ 3115] [depth= 14] . ( 13 sec) [ -17679.4342] [ 3107] [depth= 4] . ( 13 sec) [ -17665.0893] [ 3107] [depth= 6] . ( 14 sec) [ -17348.4267] [ 3054] [depth= 9] . ( 14 sec) [ -16794.2577] [ 2888] [depth= 15] . ( 15 sec) [ -16758.2749] [ 2889] [depth= 14] . ( 15 sec) [ -16741.3498] [ 2880] [depth= 1] . ( 16 sec) [ -16695.6734] [ 2861] [depth= 3] . ( 16 sec) [ -16630.9385] [ 2853] [depth= 3] . ( 17 sec) [ -16626.0420] [ 2855] [depth= 1] . ( 17 sec) [ -16484.6912] [ 2812] [depth= 5] . ( 18 sec) [ -16109.6342] [ 2740] [depth= 4] . ( 19 sec) [ -16100.2989] [ 2728] [depth= 1] . ( 19 sec) [ -16043.1452] [ 2723] [depth= 11] . ( 20 sec) [ -15725.6904] [ 2662] [depth= 10] . ( 20 sec) [ -15616.4256] [ 2624] [depth= 1] . ( 20 sec) [ -15527.9821] [ 2612] [depth= 2] . ( 21 sec) [ -15299.2151] [ 2562] [depth= 9] . ( 22 sec) [ -14515.8439] [ 2515] [depth= 11] . ( 22 sec) [ -14419.6562] [ 2496] [depth= 2] . ( 23 sec) [ -14299.8340] [ 2450] [depth= 1] . ( 23 sec) [ -14076.7394] [ 2401] [depth= 10] . ( 24 sec) [ -13980.1267] [ 2381] [depth= 1] . ( 25 sec) [ -13871.8748] [ 2354] [depth= 9] . ( 26 sec) [ -13863.5411] [ 2349] [depth= 1] . ( 26 sec) [ -13818.4652] [ 2324] [depth= 2] . ( 27 sec) [ -13748.0950] [ 2305] [depth= 6] . ( 27 sec) [ -13745.8038] [ 2309] [depth= 1] . ( 28 sec) [ -13511.6047] [ 2245] [depth= 9] . ( 30 sec) [ -13500.4495] [ 2243] [depth= 1] . ( 30 sec) [ -13455.1594] [ 2245] [depth= 3] . ( 30 sec) [ -13451.9634] [ 2247] [depth= 1] . ( 32 sec) [ -13395.8272] [ 2224] [depth= 5] . ( 32 sec) [ -13374.7936] [ 2222] [depth= 1] . ( 33 sec) [ -13339.3712] [ 2212] [depth= 2] . ( 33 sec) [ -13339.0342] [ 2208] [depth= 4] . ( 34 sec) [ -13255.2425] [ 2176] [depth= 1] . ( 34 sec) [ -13191.7060] [ 2160] [depth= 2] . ( 36 sec) [ -13119.6431] [ 2142] [depth= 1] . ( 36 sec) [ -13107.8914] [ 2141] [depth= 1] . ( 38 sec) [ -13078.6267] [ 2118] [depth= 3] . ( 38 sec) [ -13035.5577] [ 2094] [depth= 2] . ( 39 sec) [ -13005.6219] [ 2097] [depth= 2] . ( 40 sec) [ -12989.0861] [ 2097] [depth= 1] . ( 41 sec) [ -12902.0963] [Branch lengths ] . ( 41 sec) [ -12889.5731] [Alpha ][ 0.688286] . ( 43 sec) [ -12859.9415] [ 2086] [depth= 1] . ( 44 sec) [ -12853.4467] [ 2086] [depth= 1] . ( 47 sec) [ -12844.0043] [ 2083] [depth= 1] . ( 47 sec) [ -12836.0991] [ 2085] [depth= 4] . ( 48 sec) [ -12833.7738] [ 2084] [depth= 1] . ( 50 sec) [ -12809.7296] [ 2075] [depth= 1] . ( 52 sec) [ -12802.6507] [ 2072] [depth= 1] . ( 53 sec) [ -12794.1362] [ 2069] [depth= 3] . ( 54 sec) [ -12786.3148] [ 2070] [depth= 1] . ( 60 sec) [ -12785.7346] [ 2076] [depth= 1] . ( 62 sec) [ -12778.0551] [ 2072] [depth= 1] . ( 63 sec) [ -12775.0724] [ 2073] [depth= 1] . ( 70 sec) [ -12687.6113] [ 2073] [depth= 2] . ( 72 sec) [ -12637.6108] [ 2076] [depth= 1] . ( 74 sec) [ -12633.6144] [ 2076] [depth= 1] . ( 75 sec) [ -12633.3734] [ 2071] [depth= 1] . ( 76 sec) [ -12612.4651] [Branch lengths ] . ( 77 sec) [ -12611.6554] [Alpha ][ 0.749083] . ( 79 sec) [ -12598.1487] [ 2070] [depth= 2] . ( 80 sec) [ -12597.4160] [ 2070] [depth= 1] . ( 85 sec) [ -12597.3397] [ 2068] [depth= 1] . ( 88 sec) [ -12596.5231] [ 2065] [depth= 2] . ( 100 sec) [ -12595.2425] [ 2069] [depth= 1] . ( 113 sec) [ -12587.0396] [Branch lengths ] . ( 113 sec) [ -12586.9731] [Alpha ][ 0.767239] . ( 151 sec) [ -12585.9389] [Branch lengths ] . ( 152 sec) [ -12585.9389] [Topology ] . ( 155 sec) [ -12585.7821] [Topology ] . ( 159 sec) [ -12585.7168] [Topology ] . ( 163 sec) [ -12585.6778] [Topology ] . ( 166 sec) [ -12585.6539] [Topology ] . ( 170 sec) [ -12585.6391] [Topology ] . ( 174 sec) [ -12585.6300] [Topology ] . ( 175 sec) [ -12585.5670] [Alpha ][ 0.785197] . ( 175 sec) [ -12585.5670] [Topology ] . ( 178 sec) [ -12585.5547] [Topology ] . ( 182 sec) [ -12585.5474] [Topology ] . ( 186 sec) [ -12585.5428] [Topology ] . ( 190 sec) [ -12585.5400] [Topology ] . ( 193 sec) [ -12585.5383] [Topology ] . ( 197 sec) [ -12585.5372] [Topology ] . ( 198 sec) [ -12585.5360] [Alpha ][ 0.787727] . ( 198 sec) [ -12585.5360] [Topology ] . ( 202 sec) [ -12585.5351] [Topology ] . ( 202 sec) [ -12585.5351] [Alpha ][ 0.787727] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12585.535083. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22189.0087] [Alpha ][ 0.500960] . ( 1 sec) [ -22047.4001] [ 3853] [depth= 7] . ( 2 sec) [ -21674.7688] [ 3772] [depth= 6] . ( 3 sec) [ -21502.9613] [ 3752] [depth= 5] . ( 3 sec) [ -21382.7212] [ 3710] [depth= 1] . ( 3 sec) [ -21198.2309] [ 3684] [depth= 4] . ( 4 sec) [ -21053.8424] [ 3665] [depth= 3] . ( 4 sec) [ -20742.1054] [ 3677] [depth= 6] . ( 5 sec) [ -20673.6589] [ 3653] [depth= 7] . ( 5 sec) [ -20127.9614] [ 3639] [depth= 1] . ( 5 sec) [ -20006.8020] [ 3629] [depth= 2] . ( 6 sec) [ -19894.4603] [ 3597] [depth= 5] . ( 6 sec) [ -19602.7447] [ 3512] [depth= 3] . ( 7 sec) [ -19503.9707] [ 3488] [depth= 16] . ( 7 sec) [ -19322.7825] [ 3432] [depth= 10] . ( 8 sec) [ -19315.0341] [ 3435] [depth= 2] . ( 8 sec) [ -19079.7709] [ 3398] [depth= 6] . ( 8 sec) [ -19018.2670] [ 3389] [depth= 1] . ( 9 sec) [ -18876.6556] [ 3332] [depth= 7] . ( 9 sec) [ -18377.2166] [ 3235] [depth= 6] . ( 10 sec) [ -18319.0321] [ 3197] [depth= 2] . ( 10 sec) [ -18264.7585] [ 3174] [depth= 6] . ( 11 sec) [ -18111.0126] [ 3145] [depth= 2] . ( 11 sec) [ -17960.5096] [ 3168] [depth= 8] . ( 12 sec) [ -17649.2202] [ 3099] [depth= 1] . ( 13 sec) [ -17597.6568] [ 3092] [depth= 2] . ( 13 sec) [ -17054.9542] [ 2980] [depth= 12] . ( 14 sec) [ -16790.3131] [ 2931] [depth= 4] . ( 15 sec) [ -16605.1043] [ 2838] [depth= 7] . ( 15 sec) [ -16254.8039] [ 2827] [depth= 1] . ( 15 sec) [ -16158.0985] [ 2795] [depth= 9] . ( 16 sec) [ -16125.9461] [ 2786] [depth= 1] . ( 17 sec) [ -15979.6877] [ 2762] [depth= 5] . ( 17 sec) [ -15953.9722] [ 2775] [depth= 8] . ( 18 sec) [ -15889.0759] [ 2768] [depth= 7] . ( 19 sec) [ -15560.2293] [ 2686] [depth= 7] . ( 20 sec) [ -15264.9806] [ 2592] [depth= 7] . ( 20 sec) [ -15228.4865] [ 2597] [depth= 3] . ( 21 sec) [ -15095.4964] [ 2572] [depth= 2] . ( 21 sec) [ -15093.7758] [ 2574] [depth= 5] . ( 22 sec) [ -14808.0170] [ 2555] [depth= 1] . ( 22 sec) [ -14589.4002] [ 2502] [depth= 1] . ( 22 sec) [ -14528.3949] [ 2486] [depth= 6] . ( 23 sec) [ -14472.5783] [ 2484] [depth= 1] . ( 24 sec) [ -14294.1722] [ 2440] [depth= 3] . ( 24 sec) [ -14207.6728] [ 2417] [depth= 4] . ( 24 sec) [ -14202.0037] [ 2414] [depth= 1] . ( 25 sec) [ -14089.5864] [ 2381] [depth= 1] . ( 25 sec) [ -14084.3230] [ 2381] [depth= 1] . ( 26 sec) [ -14076.2430] [ 2387] [depth= 3] . ( 26 sec) [ -14054.5394] [ 2380] [depth= 1] . ( 27 sec) [ -14054.4860] [ 2381] [depth= 3] . ( 27 sec) [ -13896.4688] [ 2338] [depth= 4] . ( 28 sec) [ -13804.0662] [ 2304] [depth= 3] . ( 28 sec) [ -13795.8122] [ 2300] [depth= 7] . ( 29 sec) [ -13736.7788] [ 2292] [depth= 11] . ( 30 sec) [ -13704.1110] [ 2289] [depth= 1] . ( 30 sec) [ -13580.4429] [ 2256] [depth= 4] . ( 31 sec) [ -13518.4776] [ 2262] [depth= 4] . ( 32 sec) [ -13508.0577] [ 2265] [depth= 1] . ( 32 sec) [ -13498.5230] [ 2264] [depth= 1] . ( 33 sec) [ -13478.8740] [ 2260] [depth= 8] . ( 34 sec) [ -13411.8403] [ 2240] [depth= 3] . ( 34 sec) [ -13400.4536] [ 2250] [depth= 1] . ( 35 sec) [ -13392.4970] [ 2240] [depth= 1] . ( 35 sec) [ -13350.0617] [ 2225] [depth= 1] . ( 36 sec) [ -13290.0556] [ 2199] [depth= 6] . ( 37 sec) [ -13244.5457] [ 2186] [depth= 1] . ( 38 sec) [ -13209.3679] [ 2199] [depth= 1] . ( 38 sec) [ -13157.7975] [ 2186] [depth= 1] . ( 39 sec) [ -13115.7348] [ 2169] [depth= 4] . ( 40 sec) [ -13103.2557] [ 2167] [depth= 1] . ( 41 sec) [ -12947.7837] [Branch lengths ] . ( 42 sec) [ -12929.1724] [Alpha ][ 0.734307] . ( 43 sec) [ -12869.6502] [ 2154] [depth= 1] . ( 45 sec) [ -12840.9500] [ 2151] [depth= 2] . ( 46 sec) [ -12762.3496] [ 2121] [depth= 1] . ( 47 sec) [ -12760.7212] [ 2117] [depth= 1] . ( 47 sec) [ -12759.8887] [ 2114] [depth= 1] . ( 49 sec) [ -12759.8643] [ 2117] [depth= 1] . ( 50 sec) [ -12719.5480] [ 2100] [depth= 2] . ( 52 sec) [ -12694.9793] [ 2091] [depth= 2] . ( 53 sec) [ -12694.0831] [ 2090] [depth= 2] . ( 54 sec) [ -12692.8859] [ 2093] [depth= 1] . ( 54 sec) [ -12690.9918] [ 2097] [depth= 1] . ( 55 sec) [ -12663.1442] [ 2087] [depth= 1] . ( 55 sec) [ -12630.1741] [ 2079] [depth= 1] . ( 56 sec) [ -12628.6834] [ 2081] [depth= 1] . ( 63 sec) [ -12625.1691] [ 2083] [depth= 1] . ( 64 sec) [ -12623.7994] [ 2078] [depth= 3] . ( 67 sec) [ -12607.2681] [ 2070] [depth= 2] . ( 68 sec) [ -12605.5209] [ 2069] [depth= 1] . ( 70 sec) [ -12604.9499] [ 2071] [depth= 1] . ( 77 sec) [ -12586.6464] [Branch lengths ] . ( 78 sec) [ -12586.3064] [Alpha ][ 0.775566] . ( 117 sec) [ -12585.9140] [Branch lengths ] . ( 117 sec) [ -12585.9140] [Topology ] . ( 121 sec) [ -12585.8623] [Topology ] . ( 124 sec) [ -12585.8384] [Topology ] . ( 128 sec) [ -12585.8243] [Topology ] . ( 132 sec) [ -12585.8157] [Topology ] . ( 135 sec) [ -12585.8104] [Topology ] . ( 139 sec) [ -12585.8072] [Topology ] . ( 140 sec) [ -12585.7940] [Alpha ][ 0.784152] . ( 140 sec) [ -12585.7940] [Topology ] . ( 144 sec) [ -12585.7903] [Topology ] . ( 147 sec) [ -12585.7882] [Topology ] . ( 151 sec) [ -12585.7868] [Topology ] . ( 155 sec) [ -12585.7860] [Topology ] . ( 155 sec) [ -12585.7859] [Alpha ][ 0.784936] . ( 155 sec) [ -12585.7859] [Topology ] . ( 159 sec) [ -12585.7853] [Topology ] . ( 160 sec) [ -12585.7853] [Alpha ][ 0.784936] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12585.785299. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -12688.8590] [Alpha ][ 0.659988] . ( 1 sec) [ -12688.8590] [Topology ] . ( 4 sec) [ -12601.2388] [Topology ] . ( 8 sec) [ -12591.8603] [Topology ] . ( 12 sec) [ -12590.3330] [Topology ] . ( 16 sec) [ -12589.7518] [Topology ] . ( 19 sec) [ -12589.4532] [Topology ] . ( 23 sec) [ -12589.2792] [Topology ] . ( 27 sec) [ -12589.1721] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -12586.5064] [Alpha ][ 0.768607] . ( 56 sec) [ -12586.5064] [Topology ] . ( 59 sec) [ -12586.1292] [Topology ] . ( 63 sec) [ -12585.9206] [Topology ] . ( 67 sec) [ -12585.7972] [Topology ] . ( 71 sec) [ -12585.7230] [Topology ] . ( 74 sec) [ -12585.6778] [Topology ] . ( 78 sec) [ -12585.6500] [Topology ] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -12585.6047] [Alpha ][ 0.784498] . ( 107 sec) [ -12585.6047] [Topology ] . ( 110 sec) [ -12585.5782] [Topology ] . ( 114 sec) [ -12585.5622] [Topology ] . ( 118 sec) [ -12585.5523] [Topology ] . ( 122 sec) [ -12585.5463] [Topology ] . ( 125 sec) [ -12585.5425] [Topology ] . ( 129 sec) [ -12585.5402] [Topology ] . Checking for NNIs, optimizing five branches... . ( 158 sec) [ -12585.5386] [Alpha ][ 0.787411] . ( 158 sec) [ -12585.5386] [Topology ] . ( 162 sec) [ -12585.5367] [Topology ] . ( 165 sec) [ -12585.5356] [Topology ] . ( 169 sec) [ -12585.5348] [Topology ] . Checking for NNIs, optimizing five branches... . ( 198 sec) [ -12585.5348] [Alpha ][ 0.788198] . ( 198 sec) [ -12585.5348] [Topology ] . ( 202 sec) [ -12585.5343] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 259 sec) [ -12688.8590] [Alpha ][ 0.659988] . ( 270 sec) [ -12684.2203] [ 2077] [depth= 1] . ( 270 sec) [ -12676.3688] [ 2073] [depth= 1] . ( 271 sec) [ -12674.9374] [ 2075] [depth= 1] . ( 271 sec) [ -12673.8585] [ 2073] [depth= 1] . ( 272 sec) [ -12665.9111] [ 2074] [depth= 2] . ( 273 sec) [ -12660.8542] [ 2079] [depth= 1] . ( 273 sec) [ -12660.0933] [ 2079] [depth= 1] . ( 274 sec) [ -12659.7274] [ 2074] [depth= 1] . ( 279 sec) [ -12659.6120] [ 2075] [depth= 1] . ( 279 sec) [ -12656.1804] [ 2074] [depth= 1] . ( 281 sec) [ -12655.2707] [ 2079] [depth= 1] . ( 284 sec) [ -12651.6896] [ 2069] [depth= 2] . ( 286 sec) [ -12638.6803] [ 2072] [depth= 1] . ( 286 sec) [ -12636.7169] [ 2068] [depth= 1] . ( 287 sec) [ -12633.4255] [ 2074] [depth= 1] . ( 288 sec) [ -12627.7603] [ 2068] [depth= 1] . ( 288 sec) [ -12627.6648] [ 2069] [depth= 3] . ( 291 sec) [ -12604.8636] [Branch lengths ] . ( 292 sec) [ -12602.7370] [Alpha ][ 0.756529] . ( 303 sec) [ -12600.2376] [ 2076] [depth= 1] . ( 308 sec) [ -12599.6229] [ 2078] [depth= 1] . ( 321 sec) [ -12599.4021] [ 2075] [depth= 1] . ( 322 sec) [ -12599.3808] [ 2078] [depth= 1] . ( 323 sec) [ -12599.0854] [ 2078] [depth= 1] . ( 330 sec) [ -12599.0589] [ 2074] [depth= 1] . ( 332 sec) [ -12592.7926] [Branch lengths ] . ( 333 sec) [ -12592.7654] [Alpha ][ 0.768650] . ( 342 sec) [ -12591.2793] [ 2067] [depth= 1] . ( 357 sec) [ -12590.9233] [ 2069] [depth= 2] . ( 361 sec) [ -12590.8398] [ 2071] [depth= 1] . ( 364 sec) [ -12590.6237] [ 2072] [depth= 2] . ( 365 sec) [ -12590.2591] [ 2069] [depth= 1] . ( 368 sec) [ -12585.8948] [Branch lengths ] . ( 369 sec) [ -12585.8629] [Alpha ][ 0.781989] . ( 407 sec) [ -12585.5989] [Branch lengths ] . ( 407 sec) [ -12585.5989] [Topology ] . ( 411 sec) [ -12585.5703] [Topology ] . ( 415 sec) [ -12585.5588] [Topology ] . ( 419 sec) [ -12585.5520] [Topology ] . ( 422 sec) [ -12585.5478] [Topology ] . ( 426 sec) [ -12585.5452] [Topology ] . ( 430 sec) [ -12585.5436] [Topology ] . ( 430 sec) [ -12585.5381] [Alpha ][ 0.787518] . ( 431 sec) [ -12585.5381] [Topology ] . ( 434 sec) [ -12585.5364] [Topology ] . ( 438 sec) [ -12585.5353] [Topology ] . ( 442 sec) [ -12585.5346] [Topology ] . ( 442 sec) [ -12585.5346] [Alpha ][ 0.788305] . ( 443 sec) [ -12585.5346] [Topology ] . ( 446 sec) [ -12585.5342] [Topology ] . ( 447 sec) [ -12585.5342] [Alpha ][ 0.788305] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12585.534289 . Log likelihood obtained after SPR moves : -12585.534159 . Log likelihood of the current tree: -12585.534159. . Printing the most likely tree in file 'proteic_M1504_37x547_2003.phy_phyml_tree.txt'... . Best log likelihood : -12585.534159 . Time used 0h7m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1535.79user 0.00system 25:46.81elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps