.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1990_35x153_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 : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 5 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 104 patterns found. (out of a total of 153 sites) . 83 sites without polymorphism (54.25%). . [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) [ -3230.6562] [Alpha ][ 0.500960] . ( 0 sec) [ -3115.1636] [ 420] [depth= 5] . ( 0 sec) [ -3076.2417] [ 414] [depth= 9] . ( 0 sec) [ -3044.2473] [ 413] [depth= 1] . ( 1 sec) [ -2940.4045] [ 413] [depth= 4] . ( 1 sec) [ -2877.1890] [ 401] [depth= 1] . ( 1 sec) [ -2847.0764] [ 396] [depth= 8] . ( 1 sec) [ -2845.0186] [ 396] [depth= 1] . ( 1 sec) [ -2828.9895] [ 394] [depth= 1] . ( 1 sec) [ -2813.4174] [ 389] [depth= 2] . ( 1 sec) [ -2793.3667] [ 385] [depth= 6] . ( 2 sec) [ -2792.4282] [ 385] [depth= 2] . ( 2 sec) [ -2760.5085] [ 385] [depth= 1] . ( 2 sec) [ -2750.1149] [ 384] [depth= 2] . ( 2 sec) [ -2748.9203] [ 384] [depth= 1] . ( 2 sec) [ -2742.0931] [ 377] [depth= 5] . ( 2 sec) [ -2672.7578] [ 376] [depth= 2] . ( 2 sec) [ -2650.4839] [ 376] [depth= 3] . ( 3 sec) [ -2631.0051] [ 377] [depth= 1] . ( 3 sec) [ -2601.2452] [ 374] [depth= 9] . ( 3 sec) [ -2583.2045] [ 371] [depth= 2] . ( 3 sec) [ -2549.2481] [ 367] [depth= 5] . ( 3 sec) [ -2516.3740] [ 360] [depth= 8] . ( 3 sec) [ -2495.8852] [ 359] [depth= 3] . ( 3 sec) [ -2495.2738] [ 358] [depth= 13] . ( 4 sec) [ -2453.7763] [ 351] [depth= 6] . ( 4 sec) [ -2385.0287] [ 329] [depth= 10] . ( 4 sec) [ -2380.5043] [ 328] [depth= 2] . ( 4 sec) [ -2336.3782] [ 319] [depth= 5] . ( 4 sec) [ -2316.0218] [ 318] [depth= 4] . ( 4 sec) [ -2284.8549] [ 312] [depth= 4] . ( 4 sec) [ -2251.8900] [ 314] [depth= 9] . ( 5 sec) [ -2246.7780] [ 313] [depth= 13] . ( 5 sec) [ -2232.8039] [ 312] [depth= 7] . ( 5 sec) [ -2194.0895] [ 312] [depth= 8] . ( 5 sec) [ -2166.8770] [ 314] [depth= 2] . ( 5 sec) [ -2118.2794] [ 301] [depth= 14] . ( 5 sec) [ -2117.7812] [ 301] [depth= 1] . ( 5 sec) [ -2095.0193] [ 294] [depth= 10] . ( 5 sec) [ -2075.9751] [ 292] [depth= 3] . ( 6 sec) [ -2075.5148] [ 292] [depth= 1] . ( 6 sec) [ -2074.5703] [ 293] [depth= 1] . ( 6 sec) [ -2070.9668] [ 292] [depth= 2] . ( 6 sec) [ -2069.7809] [ 292] [depth= 1] . ( 7 sec) [ -2068.9680] [ 292] [depth= 2] . ( 8 sec) [ -2040.5757] [ 296] [depth= 4] . ( 8 sec) [ -2040.3633] [ 295] [depth= 1] . ( 9 sec) [ -2008.8394] [ 290] [depth= 2] . ( 9 sec) [ -1967.3393] [ 287] [depth= 2] . ( 9 sec) [ -1945.9853] [ 280] [depth= 7] . ( 9 sec) [ -1881.2910] [ 267] [depth= 1] . ( 9 sec) [ -1879.5447] [ 264] [depth= 4] . ( 9 sec) [ -1844.5364] [ 256] [depth= 1] . ( 10 sec) [ -1841.6782] [ 255] [depth= 3] . ( 10 sec) [ -1829.9069] [ 256] [depth= 9] . ( 10 sec) [ -1783.5560] [ 255] [depth= 3] . ( 10 sec) [ -1776.7694] [ 257] [depth= 4] . ( 11 sec) [ -1704.0769] [ 238] [depth= 5] . ( 11 sec) [ -1691.2147] [ 233] [depth= 3] . ( 11 sec) [ -1653.9801] [ 217] [depth= 6] . ( 11 sec) [ -1628.4145] [ 217] [depth= 2] . ( 11 sec) [ -1627.8376] [ 217] [depth= 1] . ( 12 sec) [ -1622.9894] [ 214] [depth= 1] . ( 12 sec) [ -1602.7873] [ 212] [depth= 3] . ( 12 sec) [ -1585.6424] [ 214] [depth= 3] . ( 12 sec) [ -1567.6071] [ 212] [depth= 2] . ( 12 sec) [ -1565.0991] [ 208] [depth= 11] . ( 13 sec) [ -1561.1472] [ 208] [depth= 1] . ( 13 sec) [ -1560.9983] [ 208] [depth= 1] . ( 13 sec) [ -1560.4598] [ 208] [depth= 1] . ( 16 sec) [ -1555.8057] [ 207] [depth= 1] . ( 19 sec) [ -1555.7253] [ 205] [depth= 1] . ( 20 sec) [ -1555.4943] [ 205] [depth= 2] . ( 20 sec) [ -1555.4145] [ 205] [depth= 1] . ( 21 sec) [ -1554.8620] [ 205] [depth= 1] . ( 21 sec) [ -1552.8542] [ 205] [depth= 1] . ( 21 sec) [ -1541.8930] [Branch lengths ] . ( 21 sec) [ -1540.8446] [Alpha ][ 0.391290] . ( 22 sec) [ -1538.4291] [ 204] [depth= 1] . ( 22 sec) [ -1500.2262] [ 195] [depth= 4] . ( 22 sec) [ -1485.1414] [ 190] [depth= 4] . ( 24 sec) [ -1480.7982] [ 189] [depth= 1] . ( 25 sec) [ -1478.7409] [ 188] [depth= 2] . ( 27 sec) [ -1478.5099] [ 188] [depth= 1] . ( 27 sec) [ -1478.4579] [ 188] [depth= 1] . ( 30 sec) [ -1477.8620] [ 189] [depth= 1] . ( 30 sec) [ -1474.6611] [ 187] [depth= 1] . ( 30 sec) [ -1474.5085] [ 187] [depth= 1] . ( 36 sec) [ -1474.4967] [ 187] [depth= 2] . ( 37 sec) [ -1471.6600] [ 187] [depth= 6] . ( 39 sec) [ -1471.3629] [ 186] [depth= 1] . ( 41 sec) [ -1468.5293] [ 187] [depth= 3] . ( 41 sec) [ -1468.4972] [ 187] [depth= 1] . ( 42 sec) [ -1467.6173] [ 187] [depth= 1] . ( 44 sec) [ -1467.3380] [ 188] [depth= 4] . ( 44 sec) [ -1467.1077] [ 188] [depth= 2] . ( 45 sec) [ -1467.0704] [ 188] [depth= 1] . ( 46 sec) [ -1467.0312] [ 188] [depth= 1] . ( 48 sec) [ -1467.0171] [ 188] [depth= 1] . ( 52 sec) [ -1466.3797] [ 183] [depth= 2] . ( 52 sec) [ -1466.3475] [ 184] [depth= 1] . ( 53 sec) [ -1466.0025] [ 184] [depth= 1] . ( 62 sec) [ -1461.6951] [Branch lengths ] . ( 63 sec) [ -1461.6621] [Alpha ][ 0.409531] . ( 80 sec) [ -1461.6033] [ 184] [depth= 1] . ( 81 sec) [ -1457.1396] [ 183] [depth= 2] . ( 81 sec) [ -1457.1239] [ 183] [depth= 1] . ( 93 sec) [ -1457.0653] [ 183] [depth= 1] . ( 111 sec) [ -1456.9758] [ 188] [depth= 3] . ( 123 sec) [ -1456.7588] [Branch lengths ] . ( 123 sec) [ -1456.7479] [Alpha ][ 0.399009] . ( 189 sec) [ -1456.5824] [Branch lengths ] . ( 189 sec) [ -1456.5824] [Topology ] . ( 190 sec) [ -1456.5252] [Topology ] . ( 191 sec) [ -1456.4826] [Topology ] . ( 192 sec) [ -1456.4515] [Topology ] . ( 193 sec) [ -1456.4242] [Topology ] . ( 194 sec) [ -1456.3997] [Topology ] . ( 195 sec) [ -1456.3830] [Topology ] . ( 195 sec) [ -1456.3826] [Alpha ][ 0.397058] . ( 196 sec) [ -1456.3826] [Topology ] . ( 196 sec) [ -1456.3765] [Topology ] . ( 197 sec) [ -1456.3750] [Topology ] . ( 198 sec) [ -1456.3747] [Topology ] . ( 199 sec) [ -1456.3747] [Alpha ][ 0.397058] . ( 199 sec) [ -1456.3747] [Topology ] . ( 200 sec) [ -1456.3745] [Topology ] . ( 200 sec) [ -1456.3745] [Alpha ][ 0.397058] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1456.374499. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3330.6388] [Alpha ][ 0.500960] . ( 1 sec) [ -3230.2980] [ 446] [depth= 1] . ( 1 sec) [ -3223.3863] [ 445] [depth= 6] . ( 1 sec) [ -3183.9143] [ 442] [depth= 5] . ( 1 sec) [ -3150.9780] [ 436] [depth= 1] . ( 1 sec) [ -3131.7562] [ 434] [depth= 7] . ( 1 sec) [ -3120.9464] [ 432] [depth= 1] . ( 1 sec) [ -3069.7106] [ 432] [depth= 1] . ( 2 sec) [ -3041.8425] [ 429] [depth= 5] . ( 2 sec) [ -3024.3746] [ 429] [depth= 3] . ( 2 sec) [ -3016.1198] [ 426] [depth= 9] . ( 2 sec) [ -2978.9102] [ 426] [depth= 2] . ( 2 sec) [ -2940.8273] [ 420] [depth= 3] . ( 2 sec) [ -2917.8600] [ 411] [depth= 4] . ( 2 sec) [ -2871.0695] [ 411] [depth= 3] . ( 3 sec) [ -2794.2720] [ 404] [depth= 3] . ( 3 sec) [ -2793.6638] [ 404] [depth= 1] . ( 3 sec) [ -2753.3632] [ 399] [depth= 6] . ( 3 sec) [ -2727.4646] [ 392] [depth= 8] . ( 3 sec) [ -2675.4192] [ 385] [depth= 5] . ( 3 sec) [ -2644.1474] [ 381] [depth= 1] . ( 3 sec) [ -2623.2917] [ 381] [depth= 1] . ( 4 sec) [ -2542.9721] [ 377] [depth= 1] . ( 4 sec) [ -2530.0760] [ 375] [depth= 12] . ( 4 sec) [ -2480.1727] [ 362] [depth= 1] . ( 4 sec) [ -2450.0503] [ 355] [depth= 11] . ( 4 sec) [ -2442.6380] [ 354] [depth= 2] . ( 5 sec) [ -2432.5893] [ 357] [depth= 1] . ( 5 sec) [ -2364.0789] [ 348] [depth= 8] . ( 5 sec) [ -2336.7765] [ 347] [depth= 11] . ( 6 sec) [ -2258.4385] [ 326] [depth= 11] . ( 6 sec) [ -2252.8039] [ 325] [depth= 1] . ( 6 sec) [ -2227.6360] [ 322] [depth= 12] . ( 6 sec) [ -2192.0966] [ 316] [depth= 2] . ( 6 sec) [ -2164.0681] [ 313] [depth= 5] . ( 6 sec) [ -2097.2368] [ 312] [depth= 5] . ( 6 sec) [ -2032.8321] [ 295] [depth= 3] . ( 7 sec) [ -2030.9049] [ 294] [depth= 1] . ( 7 sec) [ -2015.8852] [ 293] [depth= 12] . ( 7 sec) [ -2015.2568] [ 293] [depth= 1] . ( 7 sec) [ -2014.6098] [ 293] [depth= 1] . ( 7 sec) [ -1987.0318] [ 287] [depth= 9] . ( 7 sec) [ -1976.9503] [ 286] [depth= 1] . ( 7 sec) [ -1895.5896] [ 269] [depth= 2] . ( 8 sec) [ -1766.5277] [ 243] [depth= 2] . ( 8 sec) [ -1680.2045] [ 220] [depth= 8] . ( 8 sec) [ -1679.4117] [ 221] [depth= 3] . ( 8 sec) [ -1675.2652] [ 221] [depth= 1] . ( 9 sec) [ -1671.3220] [ 225] [depth= 1] . ( 9 sec) [ -1671.0416] [ 225] [depth= 2] . ( 9 sec) [ -1670.5402] [ 225] [depth= 1] . ( 9 sec) [ -1667.1790] [ 225] [depth= 1] . ( 9 sec) [ -1664.7637] [ 224] [depth= 2] . ( 9 sec) [ -1662.6881] [ 224] [depth= 1] . ( 9 sec) [ -1651.1640] [ 219] [depth= 2] . ( 10 sec) [ -1651.0949] [ 218] [depth= 2] . ( 10 sec) [ -1627.7467] [ 214] [depth= 5] . ( 10 sec) [ -1607.5868] [ 215] [depth= 1] . ( 10 sec) [ -1597.4784] [ 214] [depth= 1] . ( 10 sec) [ -1594.9868] [ 213] [depth= 1] . ( 10 sec) [ -1593.6299] [ 209] [depth= 2] . ( 10 sec) [ -1573.0567] [ 205] [depth= 1] . ( 11 sec) [ -1549.6787] [ 200] [depth= 5] . ( 11 sec) [ -1547.9592] [ 200] [depth= 2] . ( 13 sec) [ -1547.8458] [ 201] [depth= 1] . ( 13 sec) [ -1535.2403] [ 199] [depth= 11] . ( 13 sec) [ -1534.7785] [ 199] [depth= 2] . ( 14 sec) [ -1526.7453] [ 199] [depth= 1] . ( 14 sec) [ -1525.6122] [ 199] [depth= 2] . ( 14 sec) [ -1524.9918] [ 199] [depth= 1] . ( 15 sec) [ -1524.8838] [ 199] [depth= 1] . ( 15 sec) [ -1524.7426] [ 199] [depth= 1] . ( 16 sec) [ -1523.8723] [ 199] [depth= 1] . ( 16 sec) [ -1523.7368] [ 198] [depth= 2] . ( 16 sec) [ -1523.4272] [ 198] [depth= 2] . ( 16 sec) [ -1521.6591] [ 197] [depth= 1] . ( 16 sec) [ -1519.0231] [ 195] [depth= 5] . ( 17 sec) [ -1500.1765] [Branch lengths ] . ( 17 sec) [ -1499.5558] [Alpha ][ 0.411836] . ( 20 sec) [ -1494.0448] [ 195] [depth= 4] . ( 20 sec) [ -1490.6385] [ 194] [depth= 1] . ( 21 sec) [ -1480.7338] [ 191] [depth= 1] . ( 23 sec) [ -1479.5996] [ 190] [depth= 1] . ( 23 sec) [ -1476.5063] [ 189] [depth= 3] . ( 28 sec) [ -1474.6990] [ 189] [depth= 1] . ( 28 sec) [ -1474.3608] [ 189] [depth= 1] . ( 30 sec) [ -1470.2792] [ 187] [depth= 1] . ( 30 sec) [ -1468.1351] [ 185] [depth= 2] . ( 30 sec) [ -1467.5218] [ 185] [depth= 1] . ( 30 sec) [ -1466.8788] [ 184] [depth= 1] . ( 32 sec) [ -1466.7267] [ 184] [depth= 1] . ( 32 sec) [ -1465.4863] [ 184] [depth= 3] . ( 33 sec) [ -1464.6412] [ 183] [depth= 3] . ( 36 sec) [ -1464.3572] [ 183] [depth= 1] . ( 43 sec) [ -1464.3238] [ 183] [depth= 2] . ( 44 sec) [ -1463.8302] [ 183] [depth= 1] . ( 49 sec) [ -1463.8154] [ 183] [depth= 1] . ( 53 sec) [ -1463.3204] [ 183] [depth= 1] . ( 56 sec) [ -1463.1809] [ 183] [depth= 1] . ( 70 sec) [ -1462.6897] [ 187] [depth= 1] . ( 71 sec) [ -1460.4375] [Branch lengths ] . ( 71 sec) [ -1460.4052] [Alpha ][ 0.393641] . ( 81 sec) [ -1460.0017] [ 186] [depth= 1] . ( 108 sec) [ -1458.7172] [ 184] [depth= 2] . ( 112 sec) [ -1458.2482] [ 184] [depth= 1] . ( 112 sec) [ -1458.1016] [ 185] [depth= 2] . ( 126 sec) [ -1457.9230] [ 185] [depth= 1] . ( 134 sec) [ -1455.1857] [Branch lengths ] . ( 134 sec) [ -1455.1851] [Alpha ][ 0.390986] . ( 145 sec) [ -1455.1711] [ 185] [depth= 1] . ( 150 sec) [ -1455.1558] [ 185] [depth= 1] . ( 152 sec) [ -1455.1126] [ 185] [depth= 1] . ( 156 sec) [ -1455.0746] [ 185] [depth= 1] . ( 197 sec) [ -1454.5891] [Branch lengths ] . ( 197 sec) [ -1454.5890] [Alpha ][ 0.392306] . ( 197 sec) [ -1454.5890] [Topology ] . ( 198 sec) [ -1454.5674] [Topology ] . ( 199 sec) [ -1454.5614] [Topology ] . ( 200 sec) [ -1454.5577] [Topology ] . ( 201 sec) [ -1454.5550] [Topology ] . ( 202 sec) [ -1454.5531] [Topology ] . ( 203 sec) [ -1454.5517] [Topology ] . ( 204 sec) [ -1454.5514] [Alpha ][ 0.393809] . ( 204 sec) [ -1454.5514] [Topology ] . ( 205 sec) [ -1454.5504] [Topology ] . ( 206 sec) [ -1454.5498] [Topology ] . ( 206 sec) [ -1454.5498] [Alpha ][ 0.394203] . ( 206 sec) [ -1454.5498] [Topology ] . ( 207 sec) [ -1454.5493] [Topology ] . ( 207 sec) [ -1454.5493] [Alpha ][ 0.394203] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1454.549319. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3331.3578] [Alpha ][ 0.500960] . ( 0 sec) [ -3286.3789] [ 449] [depth= 6] . ( 0 sec) [ -3178.7777] [ 443] [depth= 6] . ( 1 sec) [ -3149.0278] [ 439] [depth= 3] . ( 1 sec) [ -3105.7926] [ 435] [depth= 1] . ( 1 sec) [ -3045.2009] [ 430] [depth= 6] . ( 1 sec) [ -2990.4539] [ 430] [depth= 3] . ( 1 sec) [ -2870.9157] [ 430] [depth= 1] . ( 1 sec) [ -2851.7761] [ 419] [depth= 12] . ( 1 sec) [ -2847.4585] [ 420] [depth= 2] . ( 1 sec) [ -2813.1458] [ 418] [depth= 7] . ( 2 sec) [ -2769.9000] [ 418] [depth= 1] . ( 2 sec) [ -2730.6996] [ 411] [depth= 3] . ( 2 sec) [ -2721.0677] [ 411] [depth= 2] . ( 2 sec) [ -2719.9228] [ 405] [depth= 6] . ( 2 sec) [ -2690.7252] [ 404] [depth= 2] . ( 2 sec) [ -2621.6129] [ 386] [depth= 11] . ( 2 sec) [ -2615.1619] [ 382] [depth= 2] . ( 3 sec) [ -2541.1101] [ 383] [depth= 2] . ( 3 sec) [ -2492.2068] [ 382] [depth= 8] . ( 3 sec) [ -2483.6943] [ 366] [depth= 2] . ( 3 sec) [ -2421.7519] [ 364] [depth= 1] . ( 3 sec) [ -2401.5304] [ 345] [depth= 3] . ( 3 sec) [ -2335.2305] [ 344] [depth= 3] . ( 3 sec) [ -2314.7757] [ 341] [depth= 8] . ( 3 sec) [ -2284.3117] [ 337] [depth= 7] . ( 4 sec) [ -2277.1902] [ 335] [depth= 1] . ( 4 sec) [ -2260.0999] [ 330] [depth= 4] . ( 5 sec) [ -2238.2103] [ 328] [depth= 4] . ( 5 sec) [ -2192.8289] [ 327] [depth= 3] . ( 5 sec) [ -2189.8966] [ 325] [depth= 8] . ( 5 sec) [ -2179.5885] [ 326] [depth= 1] . ( 5 sec) [ -2104.5403] [ 308] [depth= 1] . ( 5 sec) [ -2095.0849] [ 307] [depth= 1] . ( 6 sec) [ -2037.5026] [ 304] [depth= 4] . ( 6 sec) [ -1965.5785] [ 279] [depth= 4] . ( 6 sec) [ -1912.2909] [ 275] [depth= 5] . ( 6 sec) [ -1891.7552] [ 268] [depth= 5] . ( 6 sec) [ -1881.5181] [ 265] [depth= 1] . ( 7 sec) [ -1880.9055] [ 270] [depth= 4] . ( 7 sec) [ -1868.5718] [ 266] [depth= 3] . ( 10 sec) [ -1866.8758] [ 266] [depth= 2] . ( 11 sec) [ -1857.2143] [ 264] [depth= 1] . ( 11 sec) [ -1843.6683] [ 257] [depth= 5] . ( 11 sec) [ -1821.1165] [ 257] [depth= 3] . ( 11 sec) [ -1814.8915] [ 255] [depth= 9] . ( 11 sec) [ -1810.8630] [ 255] [depth= 1] . ( 12 sec) [ -1810.6803] [ 255] [depth= 2] . ( 12 sec) [ -1780.0655] [ 246] [depth= 3] . ( 13 sec) [ -1753.8330] [ 240] [depth= 1] . ( 13 sec) [ -1751.2354] [ 240] [depth= 1] . ( 13 sec) [ -1748.7801] [ 239] [depth= 2] . ( 13 sec) [ -1747.2491] [ 239] [depth= 2] . ( 13 sec) [ -1743.6690] [ 241] [depth= 1] . ( 13 sec) [ -1743.6033] [ 241] [depth= 1] . ( 14 sec) [ -1736.0782] [ 241] [depth= 1] . ( 14 sec) [ -1734.2757] [ 241] [depth= 2] . ( 14 sec) [ -1734.0457] [ 241] [depth= 1] . ( 14 sec) [ -1728.5633] [ 241] [depth= 1] . ( 14 sec) [ -1726.3416] [ 237] [depth= 3] . ( 14 sec) [ -1722.5401] [ 236] [depth= 1] . ( 15 sec) [ -1720.5535] [ 238] [depth= 2] . ( 15 sec) [ -1718.8186] [ 236] [depth= 1] . ( 16 sec) [ -1701.6743] [ 231] [depth= 1] . ( 16 sec) [ -1700.8981] [ 231] [depth= 1] . ( 16 sec) [ -1699.3486] [ 231] [depth= 1] . ( 17 sec) [ -1695.3234] [ 229] [depth= 3] . ( 18 sec) [ -1690.9293] [ 229] [depth= 1] . ( 18 sec) [ -1683.3963] [ 225] [depth= 1] . ( 18 sec) [ -1682.5199] [ 224] [depth= 1] . ( 18 sec) [ -1678.1547] [ 224] [depth= 3] . ( 18 sec) [ -1675.2784] [ 224] [depth= 1] . ( 19 sec) [ -1669.6716] [ 222] [depth= 2] . ( 19 sec) [ -1621.4177] [ 210] [depth= 5] . ( 20 sec) [ -1619.8567] [ 210] [depth= 1] . ( 20 sec) [ -1619.7995] [ 210] [depth= 2] . ( 21 sec) [ -1585.8767] [Branch lengths ] . ( 21 sec) [ -1584.8208] [Alpha ][ 0.393911] . ( 21 sec) [ -1584.2574] [ 209] [depth= 1] . ( 21 sec) [ -1583.7301] [ 208] [depth= 1] . ( 21 sec) [ -1580.9206] [ 207] [depth= 2] . ( 22 sec) [ -1580.9015] [ 206] [depth= 1] . ( 22 sec) [ -1580.3645] [ 206] [depth= 1] . ( 22 sec) [ -1580.3271] [ 206] [depth= 1] . ( 24 sec) [ -1580.2315] [ 206] [depth= 1] . ( 24 sec) [ -1571.3429] [ 204] [depth= 6] . ( 24 sec) [ -1565.8457] [ 201] [depth= 4] . ( 24 sec) [ -1551.4964] [ 204] [depth= 1] . ( 25 sec) [ -1546.7624] [ 202] [depth= 2] . ( 25 sec) [ -1500.1050] [ 194] [depth= 3] . ( 25 sec) [ -1487.1673] [ 189] [depth= 2] . ( 26 sec) [ -1485.4198] [ 189] [depth= 1] . ( 26 sec) [ -1482.9669] [ 189] [depth= 1] . ( 28 sec) [ -1482.8339] [ 189] [depth= 1] . ( 29 sec) [ -1482.4130] [ 190] [depth= 1] . ( 30 sec) [ -1482.0701] [ 189] [depth= 1] . ( 30 sec) [ -1482.0109] [ 189] [depth= 1] . ( 31 sec) [ -1480.4819] [ 186] [depth= 2] . ( 32 sec) [ -1472.0303] [ 185] [depth= 3] . ( 32 sec) [ -1468.0145] [ 184] [depth= 2] . ( 34 sec) [ -1463.9514] [ 182] [depth= 1] . ( 34 sec) [ -1462.2221] [ 183] [depth= 1] . ( 34 sec) [ -1462.2050] [ 183] [depth= 1] . ( 35 sec) [ -1462.0882] [ 183] [depth= 1] . ( 36 sec) [ -1460.3856] [ 181] [depth= 3] . ( 43 sec) [ -1455.9247] [ 180] [depth= 1] . ( 43 sec) [ -1455.8508] [ 180] [depth= 1] . ( 46 sec) [ -1454.4078] [ 179] [depth= 1] . ( 59 sec) [ -1454.3616] [ 179] [depth= 2] . ( 59 sec) [ -1449.8420] [Branch lengths ] . ( 59 sec) [ -1449.8303] [Alpha ][ 0.404593] . ( 79 sec) [ -1449.7851] [ 183] [depth= 1] . ( 114 sec) [ -1449.5832] [Branch lengths ] . ( 114 sec) [ -1449.5684] [Alpha ][ 0.392402] . ( 114 sec) [ -1449.5684] [Topology ] . ( 115 sec) [ -1449.4949] [Topology ] . ( 116 sec) [ -1449.4403] [Topology ] . ( 117 sec) [ -1449.3988] [Topology ] . ( 118 sec) [ -1449.3615] [Topology ] . ( 119 sec) [ -1449.3357] [Topology ] . ( 120 sec) [ -1449.3271] [Topology ] . ( 120 sec) [ -1449.3264] [Alpha ][ 0.389666] . ( 120 sec) [ -1449.3264] [Topology ] . ( 121 sec) [ -1449.3240] [Topology ] . ( 122 sec) [ -1449.3234] [Topology ] . ( 122 sec) [ -1449.3234] [Alpha ][ 0.389131] . ( 122 sec) [ -1449.3234] [Topology ] . ( 123 sec) [ -1449.3232] [Topology ] . ( 124 sec) [ -1449.3232] [Alpha ][ 0.389131] . Checking for NNIs, optimizing five branches... . ( 130 sec) [ -1449.2392] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1449.239244. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3334.0917] [Alpha ][ 0.500960] . ( 0 sec) [ -3282.6543] [ 465] [depth= 2] . ( 0 sec) [ -3245.9370] [ 458] [depth= 8] . ( 0 sec) [ -3227.4230] [ 457] [depth= 1] . ( 1 sec) [ -3225.4417] [ 457] [depth= 3] . ( 1 sec) [ -3208.4528] [ 453] [depth= 1] . ( 1 sec) [ -3145.2720] [ 448] [depth= 4] . ( 1 sec) [ -3129.9112] [ 445] [depth= 1] . ( 1 sec) [ -3076.2804] [ 442] [depth= 3] . ( 1 sec) [ -3002.6174] [ 440] [depth= 2] . ( 1 sec) [ -2985.7832] [ 439] [depth= 3] . ( 1 sec) [ -2922.5062] [ 423] [depth= 6] . ( 2 sec) [ -2893.3046] [ 422] [depth= 3] . ( 2 sec) [ -2866.0121] [ 421] [depth= 8] . ( 2 sec) [ -2841.8347] [ 420] [depth= 5] . ( 2 sec) [ -2807.6405] [ 411] [depth= 4] . ( 2 sec) [ -2795.8468] [ 410] [depth= 4] . ( 2 sec) [ -2736.9091] [ 403] [depth= 11] . ( 2 sec) [ -2735.0731] [ 403] [depth= 1] . ( 3 sec) [ -2722.5227] [ 402] [depth= 2] . ( 3 sec) [ -2708.7092] [ 400] [depth= 4] . ( 3 sec) [ -2680.1346] [ 395] [depth= 13] . ( 3 sec) [ -2588.1477] [ 370] [depth= 13] . ( 3 sec) [ -2544.9244] [ 362] [depth= 8] . ( 3 sec) [ -2536.1894] [ 362] [depth= 2] . ( 3 sec) [ -2449.7928] [ 349] [depth= 14] . ( 4 sec) [ -2420.6263] [ 352] [depth= 1] . ( 4 sec) [ -2394.9828] [ 351] [depth= 12] . ( 4 sec) [ -2308.0330] [ 328] [depth= 9] . ( 4 sec) [ -2282.2840] [ 324] [depth= 2] . ( 4 sec) [ -2255.5957] [ 321] [depth= 1] . ( 4 sec) [ -2243.5843] [ 319] [depth= 2] . ( 4 sec) [ -2137.0615] [ 299] [depth= 10] . ( 5 sec) [ -2035.8088] [ 298] [depth= 16] . ( 5 sec) [ -2035.2940] [ 297] [depth= 1] . ( 5 sec) [ -2035.1813] [ 297] [depth= 1] . ( 5 sec) [ -2034.0410] [ 297] [depth= 1] . ( 5 sec) [ -2029.5660] [ 294] [depth= 3] . ( 5 sec) [ -2027.2391] [ 294] [depth= 2] . ( 6 sec) [ -2014.7691] [ 293] [depth= 2] . ( 6 sec) [ -2013.4901] [ 294] [depth= 1] . ( 6 sec) [ -2006.9034] [ 291] [depth= 1] . ( 6 sec) [ -2003.9113] [ 289] [depth= 2] . ( 6 sec) [ -1938.9907] [ 275] [depth= 2] . ( 7 sec) [ -1937.4278] [ 275] [depth= 2] . ( 7 sec) [ -1932.6482] [ 276] [depth= 1] . ( 7 sec) [ -1885.6161] [ 260] [depth= 7] . ( 8 sec) [ -1884.4554] [ 260] [depth= 2] . ( 8 sec) [ -1881.9917] [ 261] [depth= 1] . ( 8 sec) [ -1858.6658] [ 257] [depth= 10] . ( 8 sec) [ -1851.1769] [ 256] [depth= 2] . ( 8 sec) [ -1789.8044] [ 245] [depth= 12] . ( 8 sec) [ -1786.0661] [ 245] [depth= 2] . ( 8 sec) [ -1783.5883] [ 245] [depth= 1] . ( 9 sec) [ -1771.3015] [ 245] [depth= 1] . ( 9 sec) [ -1766.8429] [ 244] [depth= 1] . ( 9 sec) [ -1745.5709] [ 237] [depth= 4] . ( 9 sec) [ -1728.9970] [ 233] [depth= 6] . ( 10 sec) [ -1722.2807] [ 232] [depth= 2] . ( 10 sec) [ -1709.9439] [ 230] [depth= 3] . ( 11 sec) [ -1707.7408] [ 229] [depth= 1] . ( 11 sec) [ -1703.4164] [ 229] [depth= 1] . ( 15 sec) [ -1621.9526] [ 207] [depth= 12] . ( 15 sec) [ -1611.8007] [ 205] [depth= 2] . ( 15 sec) [ -1583.5842] [ 190] [depth= 2] . ( 15 sec) [ -1582.2516] [ 193] [depth= 2] . ( 15 sec) [ -1577.7233] [ 196] [depth= 2] . ( 15 sec) [ -1575.3095] [ 195] [depth= 1] . ( 16 sec) [ -1564.5562] [ 195] [depth= 6] . ( 16 sec) [ -1562.9554] [ 195] [depth= 1] . ( 17 sec) [ -1561.1707] [ 195] [depth= 1] . ( 17 sec) [ -1561.0010] [ 195] [depth= 1] . ( 17 sec) [ -1560.4078] [ 195] [depth= 1] . ( 17 sec) [ -1554.5573] [ 194] [depth= 4] . ( 17 sec) [ -1553.1148] [ 194] [depth= 1] . ( 17 sec) [ -1498.2020] [ 190] [depth= 2] . ( 19 sec) [ -1498.1232] [ 190] [depth= 2] . ( 19 sec) [ -1497.4502] [ 190] [depth= 1] . ( 20 sec) [ -1474.9046] [Branch lengths ] . ( 20 sec) [ -1474.1097] [Alpha ][ 0.398005] . ( 22 sec) [ -1473.8139] [ 189] [depth= 1] . ( 23 sec) [ -1473.7960] [ 189] [depth= 1] . ( 24 sec) [ -1473.1760] [ 188] [depth= 1] . ( 26 sec) [ -1467.3640] [ 184] [depth= 1] . ( 29 sec) [ -1466.1186] [ 184] [depth= 1] . ( 32 sec) [ -1463.7972] [ 184] [depth= 3] . ( 33 sec) [ -1463.7773] [ 184] [depth= 1] . ( 34 sec) [ -1461.0048] [ 181] [depth= 3] . ( 36 sec) [ -1459.1857] [ 181] [depth= 2] . ( 38 sec) [ -1458.7878] [ 186] [depth= 3] . ( 41 sec) [ -1457.3783] [ 187] [depth= 1] . ( 57 sec) [ -1457.2555] [ 187] [depth= 1] . ( 58 sec) [ -1450.7777] [ 185] [depth= 5] . ( 58 sec) [ -1450.7381] [ 184] [depth= 1] . ( 61 sec) [ -1450.6185] [ 184] [depth= 1] . ( 62 sec) [ -1450.6083] [ 184] [depth= 2] . ( 69 sec) [ -1449.1480] [Branch lengths ] . ( 69 sec) [ -1449.1421] [Alpha ][ 0.390520] . ( 127 sec) [ -1448.9234] [Branch lengths ] . ( 127 sec) [ -1448.9234] [Topology ] . ( 128 sec) [ -1448.8693] [Topology ] . ( 129 sec) [ -1448.8272] [Topology ] . ( 130 sec) [ -1448.7928] [Topology ] . ( 131 sec) [ -1448.7613] [Topology ] . ( 132 sec) [ -1448.7326] [Topology ] . ( 133 sec) [ -1448.7109] [Topology ] . ( 133 sec) [ -1448.7109] [Alpha ][ 0.391331] . ( 133 sec) [ -1448.7109] [Topology ] . ( 134 sec) [ -1448.7009] [Topology ] . ( 135 sec) [ -1448.6969] [Topology ] . ( 136 sec) [ -1448.6945] [Topology ] . ( 137 sec) [ -1448.6926] [Topology ] . ( 138 sec) [ -1448.6910] [Topology ] . ( 139 sec) [ -1448.6894] [Topology ] . ( 140 sec) [ -1448.6894] [Alpha ][ 0.391723] . ( 140 sec) [ -1448.6894] [Topology ] . ( 141 sec) [ -1448.6885] [Topology ] . ( 141 sec) [ -1448.6885] [Alpha ][ 0.391723] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1448.688539. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3250.3913] [Alpha ][ 0.500960] . ( 1 sec) [ -3213.9204] [ 449] [depth= 7] . ( 1 sec) [ -3141.6636] [ 448] [depth= 5] . ( 1 sec) [ -3114.2518] [ 446] [depth= 3] . ( 1 sec) [ -3107.9105] [ 445] [depth= 1] . ( 1 sec) [ -3076.6035] [ 443] [depth= 6] . ( 1 sec) [ -3019.0205] [ 434] [depth= 3] . ( 2 sec) [ -3010.5019] [ 434] [depth= 1] . ( 2 sec) [ -2976.7335] [ 429] [depth= 4] . ( 2 sec) [ -2938.5896] [ 429] [depth= 5] . ( 2 sec) [ -2938.5408] [ 429] [depth= 6] . ( 2 sec) [ -2914.7095] [ 429] [depth= 1] . ( 2 sec) [ -2840.1039] [ 414] [depth= 8] . ( 2 sec) [ -2758.5598] [ 396] [depth= 4] . ( 3 sec) [ -2710.6400] [ 381] [depth= 7] . ( 3 sec) [ -2673.1116] [ 380] [depth= 3] . ( 3 sec) [ -2614.1234] [ 372] [depth= 1] . ( 3 sec) [ -2533.4504] [ 356] [depth= 3] . ( 3 sec) [ -2500.6601] [ 347] [depth= 6] . ( 3 sec) [ -2492.5404] [ 347] [depth= 1] . ( 3 sec) [ -2448.5219] [ 334] [depth= 2] . ( 4 sec) [ -2406.0140] [ 328] [depth= 5] . ( 4 sec) [ -2363.0749] [ 322] [depth= 8] . ( 4 sec) [ -2334.4484] [ 319] [depth= 3] . ( 4 sec) [ -2256.9356] [ 308] [depth= 5] . ( 4 sec) [ -2256.8995] [ 308] [depth= 10] . ( 4 sec) [ -2218.2325] [ 298] [depth= 9] . ( 4 sec) [ -2191.6054] [ 296] [depth= 4] . ( 5 sec) [ -2057.9457] [ 293] [depth= 3] . ( 5 sec) [ -1986.0101] [ 274] [depth= 2] . ( 5 sec) [ -1960.5676] [ 273] [depth= 3] . ( 5 sec) [ -1947.5482] [ 273] [depth= 1] . ( 5 sec) [ -1924.5806] [ 268] [depth= 1] . ( 5 sec) [ -1921.7942] [ 269] [depth= 2] . ( 6 sec) [ -1889.4154] [ 261] [depth= 5] . ( 6 sec) [ -1815.7769] [ 243] [depth= 3] . ( 7 sec) [ -1803.4334] [ 241] [depth= 2] . ( 7 sec) [ -1802.5166] [ 239] [depth= 5] . ( 7 sec) [ -1801.1105] [ 238] [depth= 2] . ( 7 sec) [ -1795.9861] [ 239] [depth= 1] . ( 8 sec) [ -1792.9208] [ 239] [depth= 5] . ( 8 sec) [ -1792.0471] [ 240] [depth= 1] . ( 8 sec) [ -1790.2106] [ 239] [depth= 7] . ( 8 sec) [ -1787.9663] [ 240] [depth= 1] . ( 9 sec) [ -1778.3530] [ 235] [depth= 11] . ( 9 sec) [ -1777.4842] [ 234] [depth= 1] . ( 9 sec) [ -1771.4008] [ 234] [depth= 1] . ( 9 sec) [ -1764.1577] [ 232] [depth= 3] . ( 9 sec) [ -1762.9578] [ 232] [depth= 1] . ( 9 sec) [ -1760.4015] [ 232] [depth= 4] . ( 10 sec) [ -1751.0528] [ 232] [depth= 1] . ( 10 sec) [ -1745.1014] [ 231] [depth= 2] . ( 10 sec) [ -1730.9440] [ 226] [depth= 3] . ( 10 sec) [ -1723.9110] [ 226] [depth= 6] . ( 10 sec) [ -1723.4511] [ 226] [depth= 1] . ( 10 sec) [ -1723.2906] [ 226] [depth= 1] . ( 11 sec) [ -1705.8469] [ 225] [depth= 1] . ( 11 sec) [ -1622.4287] [ 225] [depth= 1] . ( 12 sec) [ -1621.4311] [ 225] [depth= 1] . ( 13 sec) [ -1619.7397] [ 224] [depth= 1] . ( 13 sec) [ -1618.2386] [ 224] [depth= 4] . ( 13 sec) [ -1617.8698] [ 226] [depth= 1] . ( 13 sec) [ -1617.8475] [ 226] [depth= 2] . ( 13 sec) [ -1617.6336] [ 226] [depth= 1] . ( 13 sec) [ -1562.6536] [ 209] [depth= 7] . ( 14 sec) [ -1555.1644] [ 205] [depth= 3] . ( 14 sec) [ -1536.5609] [ 202] [depth= 1] . ( 14 sec) [ -1525.5690] [ 199] [depth= 8] . ( 14 sec) [ -1521.5361] [ 195] [depth= 5] . ( 15 sec) [ -1521.1951] [ 194] [depth= 2] . ( 18 sec) [ -1521.1567] [ 194] [depth= 1] . ( 18 sec) [ -1519.6764] [ 194] [depth= 4] . ( 18 sec) [ -1495.0242] [Branch lengths ] . ( 18 sec) [ -1494.3483] [Alpha ][ 0.408527] . ( 21 sec) [ -1486.0642] [ 189] [depth= 7] . ( 22 sec) [ -1481.5705] [ 188] [depth= 2] . ( 22 sec) [ -1481.2450] [ 188] [depth= 1] . ( 22 sec) [ -1474.9243] [ 185] [depth= 2] . ( 22 sec) [ -1474.5369] [ 185] [depth= 1] . ( 22 sec) [ -1470.3111] [ 183] [depth= 3] . ( 23 sec) [ -1470.1451] [ 183] [depth= 1] . ( 23 sec) [ -1470.1267] [ 183] [depth= 1] . ( 34 sec) [ -1466.5047] [ 182] [depth= 3] . ( 46 sec) [ -1466.3224] [ 182] [depth= 1] . ( 47 sec) [ -1466.1780] [ 182] [depth= 1] . ( 51 sec) [ -1466.1249] [ 182] [depth= 1] . ( 51 sec) [ -1466.0865] [ 182] [depth= 1] . ( 53 sec) [ -1464.2078] [ 181] [depth= 2] . ( 53 sec) [ -1459.5956] [ 180] [depth= 1] . ( 59 sec) [ -1459.4254] [ 180] [depth= 1] . ( 61 sec) [ -1459.3486] [ 184] [depth= 1] . ( 67 sec) [ -1454.7850] [Branch lengths ] . ( 67 sec) [ -1454.7788] [Alpha ][ 0.400632] . ( 96 sec) [ -1454.3611] [ 185] [depth= 2] . ( 129 sec) [ -1454.0368] [Branch lengths ] . ( 129 sec) [ -1454.0357] [Alpha ][ 0.397114] . ( 129 sec) [ -1454.0357] [Topology ] . ( 130 sec) [ -1453.9890] [Topology ] . ( 131 sec) [ -1453.9585] [Topology ] . ( 132 sec) [ -1453.9339] [Topology ] . ( 133 sec) [ -1453.9218] [Topology ] . ( 134 sec) [ -1453.9181] [Topology ] . ( 135 sec) [ -1453.9172] [Topology ] . ( 135 sec) [ -1453.9171] [Alpha ][ 0.398362] . ( 135 sec) [ -1453.9171] [Topology ] . ( 136 sec) [ -1453.9168] [Topology ] . ( 136 sec) [ -1453.9168] [Alpha ][ 0.398761] . Checking for NNIs, optimizing five branches... . ( 144 sec) [ -1453.9167] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1453.916681. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -1475.6886] [Alpha ][ 0.500960] . ( 1 sec) [ -1475.6886] [Topology ] . ( 2 sec) [ -1458.9478] [Topology ] . ( 3 sec) [ -1456.3850] [Topology ] . ( 4 sec) [ -1455.6479] [Topology ] . ( 5 sec) [ -1455.3351] [Topology ] . ( 6 sec) [ -1455.1478] [Topology ] . ( 7 sec) [ -1455.0229] [Topology ] . ( 8 sec) [ -1454.9621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -1454.8907] [Topology ] . ( 16 sec) [ -1454.4162] [Alpha ][ 0.419100] . ( 16 sec) [ -1454.4162] [Topology ] . ( 17 sec) [ -1454.3127] [Topology ] . ( 18 sec) [ -1454.2962] [Topology ] . ( 19 sec) [ -1454.2898] [Topology ] . ( 20 sec) [ -1454.2869] [Topology ] . ( 21 sec) [ -1454.2855] [Topology ] . ( 22 sec) [ -1454.2845] [Topology ] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -1454.2697] [Alpha ][ 0.406420] . ( 29 sec) [ -1454.2697] [Topology ] . ( 30 sec) [ -1454.2659] [Topology ] . ( 31 sec) [ -1454.2653] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -1454.2647] [Alpha ][ 0.403661] . ( 39 sec) [ -1454.2647] [Topology ] . ( 40 sec) [ -1454.2640] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -1454.2639] [Alpha ][ 0.403166] . ( 47 sec) [ -1454.2639] [Topology ] . ( 48 sec) [ -1454.2635] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 63 sec) [ -1475.6886] [Alpha ][ 0.500960] . ( 65 sec) [ -1475.5479] [ 181] [depth= 1] . ( 66 sec) [ -1474.1794] [ 180] [depth= 2] . ( 72 sec) [ -1473.3210] [ 180] [depth= 2] . ( 72 sec) [ -1468.9409] [ 183] [depth= 1] . ( 72 sec) [ -1466.3719] [ 180] [depth= 1] . ( 72 sec) [ -1466.1893] [ 180] [depth= 2] . ( 72 sec) [ -1465.7909] [ 180] [depth= 2] . ( 81 sec) [ -1465.7130] [ 180] [depth= 1] . ( 98 sec) [ -1465.4483] [ 181] [depth= 1] . ( 98 sec) [ -1464.5404] [ 180] [depth= 1] . ( 98 sec) [ -1464.1279] [ 180] [depth= 1] . ( 103 sec) [ -1464.0944] [ 180] [depth= 1] . ( 105 sec) [ -1463.9398] [ 180] [depth= 1] . ( 106 sec) [ -1463.2948] [ 180] [depth= 1] . ( 113 sec) [ -1458.0849] [Branch lengths ] . ( 114 sec) [ -1457.8962] [Alpha ][ 0.446406] . ( 123 sec) [ -1457.8769] [ 180] [depth= 2] . ( 126 sec) [ -1457.8074] [ 185] [depth= 3] . ( 128 sec) [ -1457.7805] [ 185] [depth= 2] . ( 133 sec) [ -1457.1222] [ 185] [depth= 1] . ( 135 sec) [ -1456.9249] [ 185] [depth= 1] . ( 171 sec) [ -1454.4562] [Branch lengths ] . ( 171 sec) [ -1454.3192] [Alpha ][ 0.406113] . ( 235 sec) [ -1454.1176] [Branch lengths ] . ( 235 sec) [ -1454.1176] [Topology ] . ( 236 sec) [ -1454.0674] [Topology ] . ( 237 sec) [ -1454.0310] [Topology ] . ( 238 sec) [ -1454.0017] [Topology ] . ( 239 sec) [ -1453.9747] [Topology ] . ( 240 sec) [ -1453.9504] [Topology ] . ( 241 sec) [ -1453.9314] [Topology ] . ( 241 sec) [ -1453.9279] [Alpha ][ 0.399938] . ( 241 sec) [ -1453.9279] [Topology ] . ( 242 sec) [ -1453.9193] [Topology ] . ( 243 sec) [ -1453.9172] [Topology ] . ( 244 sec) [ -1453.9166] [Topology ] . ( 244 sec) [ -1453.9166] [Alpha ][ 0.398949] . ( 244 sec) [ -1453.9166] [Topology ] . ( 245 sec) [ -1453.9164] [Topology ] . ( 245 sec) [ -1453.9164] [Alpha ][ 0.398949] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1454.263454 . Log likelihood obtained after SPR moves : -1453.916361 . Log likelihood of the current tree: -1453.916361. . Printing the most likely tree in file 'proteic_M1990_35x153_2004.phy_phyml_tree.txt'... . Best log likelihood : -1448.688539 . Time used 0h4m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1110.73user 0.00system 18:33.29elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps