.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data84.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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... . 161 patterns found. (out of a total of 500 sites) . 326 sites without polymorphism (65.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5461.1842] [GTR parameters ] . ( 0 sec) [ -5372.1396] [Alpha ][ 0.500960] . ( 0 sec) [ -5285.5578] [ 575] [depth= 7] . ( 0 sec) [ -5177.9087] [ 561] [depth= 5] . ( 0 sec) [ -5142.8932] [ 558] [depth= 6] . ( 0 sec) [ -5136.3567] [ 558] [depth= 5] . ( 0 sec) [ -5069.2700] [ 545] [depth= 3] . ( 0 sec) [ -5050.4609] [ 545] [depth= 1] . ( 0 sec) [ -5050.3495] [ 544] [depth= 9] . ( 1 sec) [ -5046.1467] [ 547] [depth= 1] . ( 1 sec) [ -5017.1217] [ 542] [depth= 2] . ( 1 sec) [ -4960.9462] [ 527] [depth= 11] . ( 1 sec) [ -4949.8370] [ 524] [depth= 15] . ( 1 sec) [ -4908.2081] [ 517] [depth= 2] . ( 1 sec) [ -4853.7309] [ 513] [depth= 5] . ( 1 sec) [ -4844.2169] [ 513] [depth= 7] . ( 1 sec) [ -4726.5501] [ 513] [depth= 3] . ( 1 sec) [ -4697.1636] [ 512] [depth= 9] . ( 1 sec) [ -4627.8621] [ 513] [depth= 6] . ( 1 sec) [ -4609.5860] [ 513] [depth= 3] . ( 1 sec) [ -4550.7239] [ 513] [depth= 12] . ( 1 sec) [ -4452.2670] [ 492] [depth= 13] . ( 1 sec) [ -4271.2016] [ 492] [depth= 2] . ( 1 sec) [ -4253.8687] [ 492] [depth= 10] . ( 1 sec) [ -4251.9462] [ 492] [depth= 4] . ( 1 sec) [ -4238.9396] [ 496] [depth= 1] . ( 1 sec) [ -4225.6931] [ 492] [depth= 1] . ( 1 sec) [ -4216.7351] [ 489] [depth= 4] . ( 1 sec) [ -3968.6190] [ 469] [depth= 8] . ( 1 sec) [ -3932.8319] [ 462] [depth= 13] . ( 1 sec) [ -3862.1928] [ 445] [depth= 4] . ( 1 sec) [ -3855.6846] [ 445] [depth= 1] . ( 1 sec) [ -3838.5836] [ 445] [depth= 3] . ( 1 sec) [ -3772.9378] [ 436] [depth= 7] . ( 1 sec) [ -3727.1642] [ 436] [depth= 1] . ( 1 sec) [ -3700.1889] [ 425] [depth= 8] . ( 1 sec) [ -3671.1494] [ 425] [depth= 1] . ( 1 sec) [ -3664.2381] [ 423] [depth= 1] . ( 1 sec) [ -3663.6734] [ 423] [depth= 1] . ( 1 sec) [ -3639.7904] [ 421] [depth= 1] . ( 1 sec) [ -3534.1577] [ 412] [depth= 12] . ( 1 sec) [ -3459.3479] [ 397] [depth= 13] . ( 1 sec) [ -3444.6929] [ 395] [depth= 10] . ( 1 sec) [ -3378.8568] [ 386] [depth= 7] . ( 1 sec) [ -3252.9313] [ 371] [depth= 7] . ( 1 sec) [ -3146.8687] [ 371] [depth= 6] . ( 1 sec) [ -3136.8032] [ 368] [depth= 11] . ( 1 sec) [ -3118.3280] [ 364] [depth= 9] . ( 1 sec) [ -3012.1411] [ 343] [depth= 4] . ( 1 sec) [ -3008.7683] [ 341] [depth= 1] . ( 1 sec) [ -2990.2863] [ 340] [depth= 9] . ( 1 sec) [ -2934.4412] [ 331] [depth= 3] . ( 1 sec) [ -2934.2069] [ 331] [depth= 1] . ( 1 sec) [ -2895.4237] [ 322] [depth= 1] . ( 1 sec) [ -2892.5332] [ 322] [depth= 1] . ( 1 sec) [ -2861.2601] [ 321] [depth= 6] . ( 1 sec) [ -2860.5154] [ 321] [depth= 2] . ( 1 sec) [ -2852.1379] [ 319] [depth= 2] . ( 1 sec) [ -2844.2389] [ 318] [depth= 2] . ( 1 sec) [ -2802.6203] [ 308] [depth= 2] . ( 1 sec) [ -2795.7441] [ 305] [depth= 6] . ( 1 sec) [ -2733.1332] [ 305] [depth= 7] . ( 1 sec) [ -2733.1112] [ 305] [depth= 1] . ( 2 sec) [ -2695.6148] [ 296] [depth= 4] . ( 2 sec) [ -2685.6889] [ 298] [depth= 1] . ( 2 sec) [ -2532.1726] [ 287] [depth= 5] . ( 2 sec) [ -2514.0121] [ 283] [depth= 5] . ( 2 sec) [ -2462.6464] [ 273] [depth= 7] . ( 2 sec) [ -2459.1663] [ 272] [depth= 1] . ( 2 sec) [ -2454.5792] [ 272] [depth= 1] . ( 2 sec) [ -2441.5822] [ 269] [depth= 7] . ( 2 sec) [ -2431.6002] [ 273] [depth= 4] . ( 2 sec) [ -2416.8193] [ 275] [depth= 1] . ( 2 sec) [ -2390.3829] [ 269] [depth= 3] . ( 2 sec) [ -2385.4619] [ 271] [depth= 1] . ( 2 sec) [ -2368.6536] [ 266] [depth= 4] . ( 2 sec) [ -2345.0856] [ 264] [depth= 4] . ( 2 sec) [ -2341.0470] [ 263] [depth= 1] . ( 2 sec) [ -2341.0123] [ 263] [depth= 1] . ( 2 sec) [ -2325.7085] [ 258] [depth= 6] . ( 2 sec) [ -2320.3367] [ 256] [depth= 1] . ( 2 sec) [ -2320.2391] [ 256] [depth= 1] . ( 3 sec) [ -2314.3538] [Branch lengths ] . ( 3 sec) [ -2311.9310] [GTR parameters ] . ( 3 sec) [ -2308.4076] [Alpha ][ 0.947733] . ( 3 sec) [ -2308.1646] [ 256] [depth= 1] . ( 3 sec) [ -2307.2124] [ 255] [depth= 2] . ( 3 sec) [ -2303.0609] [ 253] [depth= 1] . ( 3 sec) [ -2302.9493] [ 253] [depth= 1] . ( 4 sec) [ -2301.0516] [ 253] [depth= 1] . ( 6 sec) [ -2300.5280] [ 253] [depth= 1] . ( 8 sec) [ -2299.7369] [Branch lengths ] . ( 8 sec) [ -2299.6258] [GTR parameters ] . ( 8 sec) [ -2299.5963] [Alpha ][ 1.015258] . ( 8 sec) [ -2299.2064] [ 253] [depth= 3] . ( 10 sec) [ -2299.0942] [ 253] [depth= 1] . ( 13 sec) [ -2298.5599] [Branch lengths ] . ( 13 sec) [ -2298.5273] [GTR parameters ] . ( 13 sec) [ -2298.5273] [Alpha ][ 1.018824] . ( 18 sec) [ -2298.4810] [Branch lengths ] . ( 29 sec) [ -2298.4810] [Branch lengths ] . ( 29 sec) [ -2298.4810] [Topology ] . ( 29 sec) [ -2298.4810] [Topology ] . ( 29 sec) [ -2298.4809] [GTR parameters ] . ( 29 sec) [ -2298.4809] [Alpha ][ 1.021454] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2298.480878. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6219.3088] [GTR parameters ] . ( 1 sec) [ -6136.3230] [Alpha ][ 0.500960] . ( 1 sec) [ -6055.9892] [ 563] [depth= 3] . ( 1 sec) [ -5925.9593] [ 549] [depth= 3] . ( 1 sec) [ -5850.6904] [ 547] [depth= 4] . ( 1 sec) [ -5835.6546] [ 546] [depth= 2] . ( 1 sec) [ -5776.8986] [ 542] [depth= 3] . ( 1 sec) [ -5764.3768] [ 542] [depth= 1] . ( 1 sec) [ -5750.8293] [ 542] [depth= 3] . ( 1 sec) [ -5413.6376] [ 542] [depth= 5] . ( 1 sec) [ -5344.7471] [ 539] [depth= 4] . ( 1 sec) [ -5248.4678] [ 539] [depth= 1] . ( 1 sec) [ -5186.8969] [ 528] [depth= 11] . ( 1 sec) [ -5165.3185] [ 528] [depth= 3] . ( 1 sec) [ -5144.3076] [ 524] [depth= 1] . ( 1 sec) [ -5110.1807] [ 523] [depth= 3] . ( 1 sec) [ -5000.6412] [ 506] [depth= 10] . ( 1 sec) [ -4977.8490] [ 506] [depth= 1] . ( 1 sec) [ -4976.1942] [ 505] [depth= 9] . ( 1 sec) [ -4960.4355] [ 496] [depth= 4] . ( 1 sec) [ -4881.8259] [ 496] [depth= 1] . ( 1 sec) [ -4877.0242] [ 496] [depth= 1] . ( 1 sec) [ -4848.0646] [ 489] [depth= 3] . ( 1 sec) [ -4677.8328] [ 460] [depth= 6] . ( 1 sec) [ -4557.8275] [ 451] [depth= 4] . ( 1 sec) [ -4496.4161] [ 442] [depth= 3] . ( 1 sec) [ -4433.5147] [ 442] [depth= 4] . ( 1 sec) [ -4425.4806] [ 441] [depth= 3] . ( 1 sec) [ -4395.0542] [ 439] [depth= 1] . ( 1 sec) [ -4330.2876] [ 437] [depth= 2] . ( 1 sec) [ -4279.3013] [ 430] [depth= 14] . ( 1 sec) [ -4059.6978] [ 435] [depth= 17] . ( 1 sec) [ -4050.1875] [ 431] [depth= 2] . ( 1 sec) [ -4005.3588] [ 421] [depth= 1] . ( 1 sec) [ -3950.1828] [ 413] [depth= 11] . ( 1 sec) [ -3931.5151] [ 407] [depth= 12] . ( 1 sec) [ -3928.3888] [ 407] [depth= 2] . ( 1 sec) [ -3917.1944] [ 407] [depth= 2] . ( 1 sec) [ -3400.4585] [ 407] [depth= 3] . ( 1 sec) [ -3289.7111] [ 395] [depth= 6] . ( 1 sec) [ -3176.3535] [ 382] [depth= 12] . ( 1 sec) [ -3175.4928] [ 382] [depth= 1] . ( 1 sec) [ -3125.0875] [ 369] [depth= 4] . ( 1 sec) [ -3029.3322] [ 360] [depth= 1] . ( 1 sec) [ -3028.6309] [ 359] [depth= 1] . ( 1 sec) [ -3007.0207] [ 352] [depth= 11] . ( 1 sec) [ -2994.2949] [ 352] [depth= 6] . ( 1 sec) [ -2970.1673] [ 353] [depth= 1] . ( 1 sec) [ -2931.6759] [ 348] [depth= 6] . ( 1 sec) [ -2931.5615] [ 348] [depth= 2] . ( 1 sec) [ -2900.7453] [ 348] [depth= 10] . ( 2 sec) [ -2888.1164] [ 353] [depth= 6] . ( 2 sec) [ -2865.0611] [ 349] [depth= 8] . ( 2 sec) [ -2853.4673] [ 347] [depth= 6] . ( 2 sec) [ -2850.0681] [ 347] [depth= 1] . ( 2 sec) [ -2776.7867] [ 357] [depth= 1] . ( 2 sec) [ -2776.7764] [ 357] [depth= 5] . ( 2 sec) [ -2776.6770] [ 357] [depth= 6] . ( 2 sec) [ -2776.3019] [ 357] [depth= 5] . ( 2 sec) [ -2713.1859] [ 342] [depth= 10] . ( 2 sec) [ -2710.7642] [ 341] [depth= 3] . ( 2 sec) [ -2691.6492] [ 337] [depth= 7] . ( 2 sec) [ -2681.0227] [ 337] [depth= 1] . ( 2 sec) [ -2670.0564] [ 337] [depth= 3] . ( 2 sec) [ -2670.0080] [ 337] [depth= 2] . ( 2 sec) [ -2656.7747] [ 333] [depth= 6] . ( 2 sec) [ -2652.4276] [ 333] [depth= 3] . ( 2 sec) [ -2612.7497] [ 322] [depth= 5] . ( 2 sec) [ -2610.1411] [ 322] [depth= 1] . ( 2 sec) [ -2532.6420] [ 299] [depth= 6] . ( 2 sec) [ -2510.3275] [ 294] [depth= 1] . ( 2 sec) [ -2501.7325] [ 293] [depth= 3] . ( 2 sec) [ -2497.1931] [ 292] [depth= 1] . ( 2 sec) [ -2488.8314] [ 292] [depth= 1] . ( 2 sec) [ -2485.8382] [ 293] [depth= 1] . ( 2 sec) [ -2485.7977] [ 293] [depth= 1] . ( 2 sec) [ -2484.4843] [ 293] [depth= 1] . ( 2 sec) [ -2484.4474] [ 292] [depth= 1] . ( 2 sec) [ -2475.8607] [ 289] [depth= 1] . ( 2 sec) [ -2382.0572] [ 268] [depth= 4] . ( 2 sec) [ -2381.6972] [ 268] [depth= 2] . ( 3 sec) [ -2377.9662] [ 267] [depth= 2] . ( 3 sec) [ -2376.8233] [ 267] [depth= 3] . ( 3 sec) [ -2376.7445] [ 267] [depth= 1] . ( 3 sec) [ -2376.3422] [ 267] [depth= 1] . ( 3 sec) [ -2361.1639] [Branch lengths ] . ( 3 sec) [ -2360.0035] [GTR parameters ] . ( 3 sec) [ -2358.2829] [Alpha ][ 0.746397] . ( 3 sec) [ -2357.1311] [ 266] [depth= 1] . ( 3 sec) [ -2314.4114] [ 256] [depth= 4] . ( 4 sec) [ -2312.4071] [ 255] [depth= 1] . ( 4 sec) [ -2310.2154] [ 254] [depth= 3] . ( 4 sec) [ -2304.4768] [ 253] [depth= 2] . ( 4 sec) [ -2302.3958] [ 253] [depth= 1] . ( 8 sec) [ -2301.2602] [Branch lengths ] . ( 8 sec) [ -2300.9740] [GTR parameters ] . ( 8 sec) [ -2300.3274] [Alpha ][ 1.011659] . ( 13 sec) [ -2298.5401] [Branch lengths ] . ( 24 sec) [ -2298.4839] [Branch lengths ] . ( 24 sec) [ -2298.4839] [Topology ] . ( 25 sec) [ -2298.4839] [Topology ] . ( 25 sec) [ -2298.4813] [GTR parameters ] . ( 25 sec) [ -2298.4808] [Alpha ][ 1.021859] . ( 25 sec) [ -2298.4808] [Topology ] . ( 25 sec) [ -2298.4808] [Topology ] . ( 25 sec) [ -2298.4808] [GTR parameters ] . ( 25 sec) [ -2298.4808] [Alpha ][ 1.021859] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2298.480759. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6277.3080] [GTR parameters ] . ( 0 sec) [ -6188.9338] [Alpha ][ 0.500960] . ( 0 sec) [ -6120.9178] [ 594] [depth= 1] . ( 0 sec) [ -6032.3277] [ 580] [depth= 4] . ( 0 sec) [ -5984.4546] [ 580] [depth= 3] . ( 0 sec) [ -5943.5675] [ 580] [depth= 2] . ( 0 sec) [ -5903.1467] [ 579] [depth= 8] . ( 0 sec) [ -5882.3401] [ 579] [depth= 6] . ( 0 sec) [ -5841.8540] [ 570] [depth= 9] . ( 0 sec) [ -5801.1335] [ 567] [depth= 9] . ( 0 sec) [ -5767.2997] [ 562] [depth= 9] . ( 0 sec) [ -5384.9826] [ 552] [depth= 14] . ( 0 sec) [ -5006.3680] [ 543] [depth= 11] . ( 0 sec) [ -4677.2441] [ 530] [depth= 16] . ( 0 sec) [ -4633.8931] [ 528] [depth= 11] . ( 0 sec) [ -4552.3897] [ 528] [depth= 1] . ( 0 sec) [ -4492.7251] [ 519] [depth= 9] . ( 0 sec) [ -4479.0164] [ 519] [depth= 1] . ( 0 sec) [ -4438.0103] [ 510] [depth= 6] . ( 0 sec) [ -4282.4707] [ 510] [depth= 1] . ( 0 sec) [ -4237.7147] [ 510] [depth= 1] . ( 0 sec) [ -4222.2415] [ 505] [depth= 5] . ( 0 sec) [ -4207.6083] [ 503] [depth= 1] . ( 0 sec) [ -4194.5553] [ 502] [depth= 1] . ( 1 sec) [ -4159.9578] [ 502] [depth= 4] . ( 1 sec) [ -4115.4492] [ 494] [depth= 10] . ( 1 sec) [ -4115.0847] [ 494] [depth= 1] . ( 1 sec) [ -4042.4617] [ 481] [depth= 3] . ( 1 sec) [ -3965.5270] [ 464] [depth= 3] . ( 1 sec) [ -3956.5148] [ 464] [depth= 8] . ( 1 sec) [ -3954.2080] [ 462] [depth= 5] . ( 1 sec) [ -3863.7891] [ 452] [depth= 10] . ( 1 sec) [ -3859.3363] [ 453] [depth= 1] . ( 1 sec) [ -3839.6359] [ 450] [depth= 10] . ( 1 sec) [ -3813.8157] [ 452] [depth= 12] . ( 1 sec) [ -3813.3853] [ 453] [depth= 2] . ( 1 sec) [ -3596.1665] [ 432] [depth= 8] . ( 1 sec) [ -3569.1634] [ 427] [depth= 3] . ( 1 sec) [ -3510.7140] [ 426] [depth= 7] . ( 1 sec) [ -3372.4163] [ 426] [depth= 9] . ( 1 sec) [ -3273.8798] [ 406] [depth= 8] . ( 1 sec) [ -3270.8620] [ 405] [depth= 3] . ( 1 sec) [ -3206.0280] [ 398] [depth= 6] . ( 1 sec) [ -3205.2080] [ 398] [depth= 1] . ( 1 sec) [ -3168.5272] [ 397] [depth= 5] . ( 1 sec) [ -3159.1986] [ 394] [depth= 1] . ( 1 sec) [ -3098.8474] [ 382] [depth= 9] . ( 1 sec) [ -3098.8246] [ 382] [depth= 1] . ( 1 sec) [ -3097.8466] [ 381] [depth= 3] . ( 1 sec) [ -3096.1003] [ 381] [depth= 3] . ( 1 sec) [ -3090.1822] [ 381] [depth= 1] . ( 1 sec) [ -3069.9824] [ 381] [depth= 2] . ( 1 sec) [ -3069.9010] [ 381] [depth= 1] . ( 1 sec) [ -3048.2411] [ 380] [depth= 1] . ( 1 sec) [ -2921.7814] [ 381] [depth= 1] . ( 1 sec) [ -2921.6729] [ 381] [depth= 6] . ( 1 sec) [ -2906.7329] [ 377] [depth= 1] . ( 1 sec) [ -2898.4026] [ 374] [depth= 2] . ( 1 sec) [ -2892.6883] [ 374] [depth= 2] . ( 1 sec) [ -2876.7828] [ 374] [depth= 4] . ( 1 sec) [ -2816.0623] [ 359] [depth= 11] . ( 1 sec) [ -2758.1591] [ 347] [depth= 5] . ( 1 sec) [ -2757.8545] [ 344] [depth= 10] . ( 1 sec) [ -2757.6291] [ 344] [depth= 3] . ( 1 sec) [ -2757.5413] [ 344] [depth= 1] . ( 1 sec) [ -2690.8321] [ 333] [depth= 6] . ( 1 sec) [ -2681.6144] [ 329] [depth= 6] . ( 1 sec) [ -2677.4781] [ 331] [depth= 1] . ( 1 sec) [ -2664.0207] [ 327] [depth= 5] . ( 1 sec) [ -2654.8118] [ 325] [depth= 3] . ( 1 sec) [ -2631.8608] [ 322] [depth= 1] . ( 2 sec) [ -2616.1553] [ 321] [depth= 3] . ( 2 sec) [ -2613.2725] [ 320] [depth= 4] . ( 2 sec) [ -2605.5904] [ 319] [depth= 3] . ( 2 sec) [ -2600.7302] [ 321] [depth= 2] . ( 2 sec) [ -2598.4073] [ 320] [depth= 1] . ( 2 sec) [ -2594.2977] [ 320] [depth= 4] . ( 2 sec) [ -2507.7730] [ 300] [depth= 1] . ( 2 sec) [ -2495.9127] [ 296] [depth= 4] . ( 2 sec) [ -2451.6656] [ 285] [depth= 2] . ( 2 sec) [ -2449.6053] [ 285] [depth= 1] . ( 2 sec) [ -2449.0737] [ 283] [depth= 3] . ( 2 sec) [ -2447.1147] [ 284] [depth= 5] . ( 2 sec) [ -2447.0915] [ 284] [depth= 2] . ( 2 sec) [ -2437.7720] [Branch lengths ] . ( 3 sec) [ -2436.7339] [GTR parameters ] . ( 3 sec) [ -2436.3229] [Alpha ][ 0.598259] . ( 3 sec) [ -2432.9640] [ 283] [depth= 1] . ( 3 sec) [ -2428.1172] [ 281] [depth= 1] . ( 3 sec) [ -2425.9269] [ 282] [depth= 1] . ( 3 sec) [ -2425.1976] [ 282] [depth= 1] . ( 3 sec) [ -2407.2289] [ 279] [depth= 3] . ( 3 sec) [ -2407.1623] [ 279] [depth= 2] . ( 3 sec) [ -2404.2640] [ 278] [depth= 1] . ( 3 sec) [ -2395.3105] [ 275] [depth= 2] . ( 3 sec) [ -2387.1258] [ 274] [depth= 4] . ( 3 sec) [ -2386.7639] [ 274] [depth= 2] . ( 3 sec) [ -2377.5648] [ 273] [depth= 2] . ( 3 sec) [ -2377.5196] [ 273] [depth= 2] . ( 4 sec) [ -2369.6291] [ 259] [depth= 2] . ( 4 sec) [ -2369.6048] [ 259] [depth= 1] . ( 4 sec) [ -2369.5692] [ 258] [depth= 4] . ( 4 sec) [ -2368.9930] [ 260] [depth= 2] . ( 4 sec) [ -2355.4786] [ 257] [depth= 2] . ( 4 sec) [ -2333.3028] [ 256] [depth= 2] . ( 4 sec) [ -2320.4519] [ 257] [depth= 1] . ( 4 sec) [ -2319.3739] [ 257] [depth= 1] . ( 4 sec) [ -2313.2221] [ 256] [depth= 2] . ( 4 sec) [ -2310.4221] [ 255] [depth= 1] . ( 5 sec) [ -2310.3558] [ 255] [depth= 1] . ( 5 sec) [ -2308.5228] [ 254] [depth= 2] . ( 5 sec) [ -2306.5776] [ 253] [depth= 1] . ( 5 sec) [ -2305.7013] [ 253] [depth= 1] . ( 5 sec) [ -2305.0526] [ 253] [depth= 1] . ( 6 sec) [ -2302.1603] [ 253] [depth= 1] . ( 6 sec) [ -2302.1326] [ 253] [depth= 1] . ( 6 sec) [ -2301.6753] [Branch lengths ] . ( 6 sec) [ -2301.2661] [GTR parameters ] . ( 6 sec) [ -2299.0484] [Alpha ][ 1.029183] . ( 10 sec) [ -2298.5353] [ 253] [depth= 3] . ( 11 sec) [ -2298.5061] [Branch lengths ] . ( 12 sec) [ -2298.4815] [GTR parameters ] . ( 12 sec) [ -2298.4812] [Alpha ][ 1.021600] . ( 23 sec) [ -2298.4808] [Branch lengths ] . ( 23 sec) [ -2298.4808] [Topology ] . ( 23 sec) [ -2298.4808] [Topology ] . ( 23 sec) [ -2298.4808] [GTR parameters ] . ( 23 sec) [ -2298.4808] [Alpha ][ 1.021600] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2298.480798. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6237.4476] [GTR parameters ] . ( 0 sec) [ -6154.6090] [Alpha ][ 0.500960] . ( 0 sec) [ -6043.1665] [ 591] [depth= 8] . ( 0 sec) [ -5939.6115] [ 577] [depth= 5] . ( 0 sec) [ -5308.0829] [ 577] [depth= 2] . ( 0 sec) [ -5248.0680] [ 577] [depth= 1] . ( 0 sec) [ -5190.0279] [ 577] [depth= 4] . ( 0 sec) [ -5141.4578] [ 576] [depth= 3] . ( 0 sec) [ -5089.0799] [ 576] [depth= 5] . ( 0 sec) [ -5074.4798] [ 576] [depth= 2] . ( 0 sec) [ -5055.7817] [ 576] [depth= 1] . ( 0 sec) [ -5020.0901] [ 576] [depth= 7] . ( 0 sec) [ -4981.7986] [ 576] [depth= 2] . ( 0 sec) [ -4884.7078] [ 559] [depth= 6] . ( 0 sec) [ -4883.2222] [ 558] [depth= 4] . ( 0 sec) [ -4856.0124] [ 558] [depth= 2] . ( 0 sec) [ -4763.7666] [ 540] [depth= 9] . ( 0 sec) [ -4626.4713] [ 540] [depth= 2] . ( 1 sec) [ -4620.8222] [ 543] [depth= 1] . ( 1 sec) [ -4494.8710] [ 523] [depth= 2] . ( 1 sec) [ -4450.7045] [ 512] [depth= 18] . ( 1 sec) [ -4423.1338] [ 511] [depth= 19] . ( 1 sec) [ -4352.5161] [ 491] [depth= 19] . ( 1 sec) [ -4265.0532] [ 477] [depth= 6] . ( 1 sec) [ -4264.5073] [ 477] [depth= 1] . ( 1 sec) [ -4249.6728] [ 474] [depth= 9] . ( 1 sec) [ -4249.6548] [ 474] [depth= 1] . ( 1 sec) [ -4229.9561] [ 466] [depth= 4] . ( 1 sec) [ -3731.8812] [ 466] [depth= 2] . ( 1 sec) [ -3727.4181] [ 465] [depth= 8] . ( 1 sec) [ -3712.7409] [ 462] [depth= 11] . ( 1 sec) [ -3619.3357] [ 462] [depth= 1] . ( 1 sec) [ -3351.4603] [ 438] [depth= 11] . ( 1 sec) [ -3325.4223] [ 438] [depth= 10] . ( 1 sec) [ -3183.6680] [ 416] [depth= 16] . ( 1 sec) [ -3102.9935] [ 398] [depth= 4] . ( 1 sec) [ -3044.5707] [ 385] [depth= 7] . ( 1 sec) [ -3025.7408] [ 378] [depth= 4] . ( 1 sec) [ -3001.9597] [ 375] [depth= 2] . ( 1 sec) [ -2988.7842] [ 373] [depth= 2] . ( 1 sec) [ -2984.4296] [ 373] [depth= 1] . ( 1 sec) [ -2968.4525] [ 373] [depth= 3] . ( 1 sec) [ -2964.6330] [ 373] [depth= 1] . ( 1 sec) [ -2921.8319] [ 363] [depth= 4] . ( 1 sec) [ -2890.3876] [ 362] [depth= 6] . ( 1 sec) [ -2875.3139] [ 363] [depth= 1] . ( 1 sec) [ -2870.6851] [ 361] [depth= 7] . ( 1 sec) [ -2805.3093] [ 346] [depth= 10] . ( 1 sec) [ -2805.2279] [ 347] [depth= 1] . ( 1 sec) [ -2768.1316] [ 338] [depth= 4] . ( 1 sec) [ -2722.8896] [ 331] [depth= 3] . ( 1 sec) [ -2720.2841] [ 330] [depth= 1] . ( 1 sec) [ -2681.8315] [ 320] [depth= 8] . ( 1 sec) [ -2663.9994] [ 315] [depth= 4] . ( 1 sec) [ -2656.9634] [ 315] [depth= 2] . ( 1 sec) [ -2656.7841] [ 316] [depth= 1] . ( 1 sec) [ -2656.4454] [ 316] [depth= 3] . ( 1 sec) [ -2621.1832] [ 306] [depth= 6] . ( 1 sec) [ -2620.4844] [ 306] [depth= 2] . ( 2 sec) [ -2612.4270] [ 305] [depth= 2] . ( 2 sec) [ -2567.7666] [ 297] [depth= 4] . ( 2 sec) [ -2552.3211] [ 296] [depth= 3] . ( 2 sec) [ -2552.2540] [ 296] [depth= 2] . ( 2 sec) [ -2551.9211] [ 298] [depth= 2] . ( 2 sec) [ -2468.2955] [ 278] [depth= 6] . ( 2 sec) [ -2466.8127] [ 279] [depth= 1] . ( 2 sec) [ -2427.4542] [ 270] [depth= 2] . ( 2 sec) [ -2426.2383] [ 269] [depth= 1] . ( 2 sec) [ -2407.4413] [ 263] [depth= 2] . ( 2 sec) [ -2406.8335] [ 263] [depth= 1] . ( 2 sec) [ -2404.1023] [ 262] [depth= 1] . ( 2 sec) [ -2395.8866] [ 261] [depth= 2] . ( 2 sec) [ -2395.2874] [ 261] [depth= 1] . ( 2 sec) [ -2395.2559] [ 261] [depth= 1] . ( 2 sec) [ -2389.5387] [ 261] [depth= 1] . ( 2 sec) [ -2375.3894] [ 257] [depth= 2] . ( 2 sec) [ -2338.6717] [Branch lengths ] . ( 3 sec) [ -2335.3593] [GTR parameters ] . ( 3 sec) [ -2332.2357] [Alpha ][ 0.881744] . ( 3 sec) [ -2313.5002] [ 257] [depth= 1] . ( 3 sec) [ -2309.9708] [ 255] [depth= 2] . ( 3 sec) [ -2309.3668] [ 254] [depth= 1] . ( 4 sec) [ -2309.3283] [ 254] [depth= 2] . ( 4 sec) [ -2309.1789] [ 254] [depth= 1] . ( 4 sec) [ -2308.1337] [ 254] [depth= 1] . ( 4 sec) [ -2308.0306] [ 254] [depth= 2] . ( 5 sec) [ -2307.7680] [ 254] [depth= 1] . ( 5 sec) [ -2307.1998] [ 254] [depth= 2] . ( 6 sec) [ -2306.4884] [ 254] [depth= 1] . ( 6 sec) [ -2306.3876] [ 254] [depth= 1] . ( 6 sec) [ -2303.1585] [ 254] [depth= 4] . ( 6 sec) [ -2302.8498] [ 254] [depth= 1] . ( 7 sec) [ -2302.1831] [Branch lengths ] . ( 7 sec) [ -2302.0516] [GTR parameters ] . ( 7 sec) [ -2301.9758] [Alpha ][ 0.981377] . ( 11 sec) [ -2299.7787] [ 253] [depth= 2] . ( 12 sec) [ -2298.5926] [Branch lengths ] . ( 12 sec) [ -2298.5841] [GTR parameters ] . ( 12 sec) [ -2298.5748] [Alpha ][ 1.020573] . ( 17 sec) [ -2298.4805] [Branch lengths ] . ( 28 sec) [ -2298.4805] [Branch lengths ] . ( 28 sec) [ -2298.4805] [Topology ] . ( 28 sec) [ -2298.4805] [Topology ] . ( 28 sec) [ -2298.4805] [GTR parameters ] . ( 28 sec) [ -2298.4805] [Alpha ][ 1.021594] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2298.480524. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6319.6026] [GTR parameters ] . ( 1 sec) [ -6226.9721] [Alpha ][ 0.500960] . ( 1 sec) [ -6139.6508] [ 594] [depth= 6] . ( 1 sec) [ -6055.7684] [ 580] [depth= 11] . ( 1 sec) [ -6050.0911] [ 580] [depth= 2] . ( 1 sec) [ -6040.2396] [ 580] [depth= 3] . ( 1 sec) [ -6032.3064] [ 579] [depth= 4] . ( 1 sec) [ -6014.5466] [ 579] [depth= 3] . ( 1 sec) [ -6014.0868] [ 579] [depth= 7] . ( 1 sec) [ -5989.4213] [ 579] [depth= 1] . ( 1 sec) [ -5929.1857] [ 573] [depth= 12] . ( 1 sec) [ -5813.8143] [ 566] [depth= 15] . ( 1 sec) [ -5729.3829] [ 547] [depth= 8] . ( 1 sec) [ -5631.8974] [ 526] [depth= 6] . ( 1 sec) [ -5373.3371] [ 505] [depth= 8] . ( 1 sec) [ -5364.7330] [ 504] [depth= 1] . ( 1 sec) [ -5348.7195] [ 502] [depth= 3] . ( 1 sec) [ -5348.5086] [ 502] [depth= 4] . ( 1 sec) [ -5170.1224] [ 502] [depth= 1] . ( 1 sec) [ -5095.5128] [ 502] [depth= 2] . ( 1 sec) [ -4935.6837] [ 502] [depth= 3] . ( 1 sec) [ -4837.9097] [ 501] [depth= 8] . ( 1 sec) [ -4749.1323] [ 484] [depth= 7] . ( 1 sec) [ -4721.1713] [ 484] [depth= 3] . ( 1 sec) [ -4656.0407] [ 473] [depth= 2] . ( 1 sec) [ -4654.6300] [ 473] [depth= 1] . ( 1 sec) [ -4556.4676] [ 470] [depth= 9] . ( 1 sec) [ -4312.0396] [ 439] [depth= 8] . ( 1 sec) [ -4311.2127] [ 439] [depth= 1] . ( 1 sec) [ -4213.3766] [ 429] [depth= 5] . ( 1 sec) [ -4197.4999] [ 429] [depth= 8] . ( 1 sec) [ -4177.1224] [ 419] [depth= 5] . ( 1 sec) [ -4120.7301] [ 406] [depth= 2] . ( 1 sec) [ -4064.6493] [ 397] [depth= 9] . ( 1 sec) [ -4056.5942] [ 396] [depth= 5] . ( 1 sec) [ -3118.9930] [ 366] [depth= 10] . ( 1 sec) [ -3099.1636] [ 360] [depth= 2] . ( 1 sec) [ -3089.8785] [ 357] [depth= 1] . ( 1 sec) [ -3061.7164] [ 356] [depth= 5] . ( 1 sec) [ -3047.5392] [ 356] [depth= 1] . ( 1 sec) [ -3023.5535] [ 355] [depth= 4] . ( 1 sec) [ -3023.5238] [ 355] [depth= 1] . ( 1 sec) [ -3011.0954] [ 353] [depth= 5] . ( 1 sec) [ -2953.6381] [ 350] [depth= 1] . ( 1 sec) [ -2907.1252] [ 338] [depth= 9] . ( 2 sec) [ -2898.9336] [ 334] [depth= 9] . ( 2 sec) [ -2894.3018] [ 327] [depth= 3] . ( 2 sec) [ -2891.3645] [ 326] [depth= 1] . ( 2 sec) [ -2889.1251] [ 330] [depth= 7] . ( 2 sec) [ -2799.2077] [ 321] [depth= 7] . ( 2 sec) [ -2768.9786] [ 318] [depth= 3] . ( 2 sec) [ -2768.8285] [ 318] [depth= 2] . ( 2 sec) [ -2707.6306] [ 305] [depth= 3] . ( 2 sec) [ -2700.2484] [ 305] [depth= 2] . ( 2 sec) [ -2669.1986] [ 305] [depth= 1] . ( 2 sec) [ -2659.7739] [ 301] [depth= 3] . ( 2 sec) [ -2643.8409] [ 301] [depth= 1] . ( 2 sec) [ -2643.5668] [ 301] [depth= 3] . ( 2 sec) [ -2643.5179] [ 301] [depth= 2] . ( 2 sec) [ -2632.9475] [ 299] [depth= 9] . ( 2 sec) [ -2622.6849] [ 298] [depth= 6] . ( 2 sec) [ -2618.4393] [ 299] [depth= 1] . ( 2 sec) [ -2617.2170] [ 299] [depth= 1] . ( 2 sec) [ -2587.2188] [ 293] [depth= 1] . ( 2 sec) [ -2584.2749] [ 292] [depth= 2] . ( 2 sec) [ -2581.6582] [ 291] [depth= 1] . ( 2 sec) [ -2573.1876] [ 291] [depth= 1] . ( 2 sec) [ -2562.1851] [ 295] [depth= 1] . ( 2 sec) [ -2561.7710] [ 296] [depth= 4] . ( 2 sec) [ -2535.7786] [ 292] [depth= 1] . ( 2 sec) [ -2517.1430] [ 284] [depth= 1] . ( 2 sec) [ -2509.9188] [ 283] [depth= 3] . ( 2 sec) [ -2503.6634] [ 281] [depth= 2] . ( 2 sec) [ -2452.0732] [ 273] [depth= 2] . ( 2 sec) [ -2452.0161] [ 273] [depth= 1] . ( 2 sec) [ -2449.6725] [ 272] [depth= 2] . ( 2 sec) [ -2446.3115] [ 271] [depth= 1] . ( 2 sec) [ -2429.0994] [ 268] [depth= 3] . ( 2 sec) [ -2400.5403] [ 269] [depth= 1] . ( 2 sec) [ -2394.9298] [ 269] [depth= 2] . ( 3 sec) [ -2394.7534] [ 269] [depth= 1] . ( 3 sec) [ -2393.8596] [ 266] [depth= 4] . ( 3 sec) [ -2392.8054] [ 266] [depth= 1] . ( 3 sec) [ -2390.7914] [ 265] [depth= 2] . ( 3 sec) [ -2359.5450] [Branch lengths ] . ( 3 sec) [ -2357.4996] [GTR parameters ] . ( 3 sec) [ -2355.6842] [Alpha ][ 0.753500] . ( 3 sec) [ -2327.8440] [ 258] [depth= 4] . ( 4 sec) [ -2322.4543] [ 256] [depth= 1] . ( 4 sec) [ -2317.9918] [ 255] [depth= 1] . ( 4 sec) [ -2317.9790] [ 255] [depth= 1] . ( 5 sec) [ -2316.8764] [ 256] [depth= 1] . ( 5 sec) [ -2309.8050] [ 255] [depth= 1] . ( 5 sec) [ -2309.7817] [ 255] [depth= 1] . ( 5 sec) [ -2307.5666] [ 254] [depth= 1] . ( 5 sec) [ -2305.3927] [ 253] [depth= 1] . ( 6 sec) [ -2305.3789] [ 253] [depth= 1] . ( 7 sec) [ -2305.3582] [ 253] [depth= 1] . ( 7 sec) [ -2305.3275] [ 253] [depth= 1] . ( 8 sec) [ -2304.4976] [Branch lengths ] . ( 8 sec) [ -2304.3581] [GTR parameters ] . ( 8 sec) [ -2303.8575] [Alpha ][ 0.982799] . ( 12 sec) [ -2303.4564] [ 253] [depth= 3] . ( 12 sec) [ -2303.3954] [ 253] [depth= 1] . ( 13 sec) [ -2301.4446] [Branch lengths ] . ( 13 sec) [ -2301.4078] [GTR parameters ] . ( 13 sec) [ -2301.4046] [Alpha ][ 1.005218] . ( 13 sec) [ -2301.3766] [ 253] [depth= 1] . ( 18 sec) [ -2298.5367] [Branch lengths ] . ( 18 sec) [ -2298.5341] [GTR parameters ] . ( 18 sec) [ -2298.5324] [Alpha ][ 1.021734] . ( 23 sec) [ -2298.4805] [Branch lengths ] . ( 34 sec) [ -2298.4805] [Branch lengths ] . ( 34 sec) [ -2298.4805] [Topology ] . ( 35 sec) [ -2298.4805] [Topology ] . ( 35 sec) [ -2298.4805] [GTR parameters ] . ( 35 sec) [ -2298.4805] [Alpha ][ 1.021734] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2298.480461. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-2307.077771 . ( 0 sec) [ -2305.6179] [GTR parameters ] . ( 0 sec) [ -2305.6153] [Alpha ][ 0.979430] . ( 0 sec) [ -2305.6153] [Topology ] . ( 1 sec) [ -2301.4733] [Topology ] . ( 1 sec) [ -2298.8976] [Topology ] . ( 1 sec) [ -2298.5891] [Topology ] . ( 2 sec) [ -2298.5280] [Topology ] . ( 2 sec) [ -2298.5139] [Topology ] . ( 2 sec) [ -2298.5104] [Topology ] . ( 2 sec) [ -2298.5095] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-2298.509471 . ( 4 sec) [ -2298.4914] [GTR parameters ] . ( 4 sec) [ -2298.4808] [Alpha ][ 1.021256] . ( 4 sec) [ -2298.4808] [Topology ] . ( 5 sec) [ -2298.4805] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-2298.480485 . ( 6 sec) [ -2298.4805] [GTR parameters ] . ( 6 sec) [ -2298.4805] [Alpha ][ 1.021256] . ( 6 sec) [ -2298.4805] [Topology ] . ( 7 sec) [ -2298.4804] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 10 sec) [ -2305.6179] [GTR parameters ] . ( 10 sec) [ -2305.6153] [Alpha ][ 0.979430] . ( 10 sec) [ -2305.5720] [ 254] [depth= 1] . ( 10 sec) [ -2305.5596] [ 254] [depth= 1] . ( 11 sec) [ -2305.2005] [ 254] [depth= 1] . ( 11 sec) [ -2305.1783] [ 254] [depth= 1] . ( 11 sec) [ -2305.1256] [ 254] [depth= 1] . ( 11 sec) [ -2305.0988] [ 254] [depth= 1] . ( 11 sec) [ -2305.0154] [ 254] [depth= 1] . ( 14 sec) [ -2302.8322] [ 254] [depth= 2] . ( 14 sec) [ -2300.3373] [ 253] [depth= 1] . ( 14 sec) [ -2299.8618] [ 253] [depth= 1] . ( 14 sec) [ -2299.6790] [ 253] [depth= 1] . ( 14 sec) [ -2299.6676] [ 253] [depth= 1] . ( 14 sec) [ -2299.5345] [ 253] [depth= 1] . ( 15 sec) [ -2299.5066] [ 253] [depth= 1] . ( 15 sec) [ -2298.5342] [Branch lengths ] . ( 15 sec) [ -2298.5161] [GTR parameters ] . ( 15 sec) [ -2298.5056] [Alpha ][ 1.020865] . ( 20 sec) [ -2298.4801] [Branch lengths ] . ( 31 sec) [ -2298.4800] [Branch lengths ] . ( 31 sec) [ -2298.4800] [Topology ] . ( 31 sec) [ -2298.4800] [Topology ] . ( 31 sec) [ -2298.4799] [GTR parameters ] . ( 31 sec) [ -2298.4799] [Alpha ][ 1.021886] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2298.480372 . Log likelihood obtained after SPR moves : -2298.479933 . Log likelihood of the current tree: -2298.479933. . Printing the most likely tree in file 'data84.phy_phyml_tree.txt'... . Best log likelihood : -2298.479933 . Time used 0h0m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo