.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M4055_306x7062_2008.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 65 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 6303 patterns found. (out of a total of 7062 sites) . 703 sites without polymorphism (9.95%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1028Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 114 sec) [ -298394.7746] [GTR parameters ] . ( 125 sec) [ -298078.9669] [Alpha ][ 0.712583] . ( 128 sec) [ -298078.9669] [Topology ] . ( 204 sec) [ -294455.0479] [Topology ] . ( 294 sec) [ -292637.4058] [Topology ] . ( 375 sec) [ -292344.5927] [Topology ] . ( 466 sec) [ -291814.2987] [Topology ] . ( 550 sec) [ -291961.4482] [Topology ] . Moving backward . ( 557 sec) [ -291224.2764] [Topology ] . ( 644 sec) [ -290743.8105] [Topology ] . ( 725 sec) [ -290999.9503] [Topology ] . Moving backward . ( 732 sec) [ -290524.9989] [Topology ] . ( 936 sec) [ -290272.0115] [GTR parameters ] . ( 946 sec) [ -290080.0507] [Alpha ][ 0.908334] . ( 948 sec) [ -290080.0507] [Topology ] . ( 1030 sec) [ -290605.5336] [Topology ] . Moving backward . ( 1037 sec) [ -289864.5214] [Topology ] . ( 1121 sec) [ -289623.0717] [Topology ] . ( 1203 sec) [ -290150.3472] [Topology ] . Moving backward . ( 1212 sec) [ -289580.2336] [Topology ] . ( 1294 sec) [ -289496.6713] [Topology ] . ( 1376 sec) [ -289915.3315] [Topology ] . Moving backward . ( 1386 sec) [ -289378.7319] [Topology ] . ( 1468 sec) [ -289407.1345] [Topology ] . Moving backward . ( 1519 sec) [ -289023.9906] [GTR parameters ] . ( 1528 sec) [ -289023.4632] [Alpha ][ 0.897213] . ( 1531 sec) [ -289023.4632] [Topology ] . ( 1611 sec) [ -288873.2617] [Topology ] . ( 1692 sec) [ -288839.0515] [Topology ] . ( 1774 sec) [ -288890.5354] [Topology ] . Moving backward . ( 1781 sec) [ -288770.5294] [Topology ] . ( 1862 sec) [ -288821.5668] [Topology ] . Moving backward . ( 1869 sec) [ -288630.1496] [Topology ] . ( 1949 sec) [ -288589.5533] [Topology ] . ( 2029 sec) [ -288636.0014] [Topology ] . Moving backward . ( 2036 sec) [ -288548.3707] [Topology ] . ( 2202 sec) [ -288519.8104] [GTR parameters ] . ( 2212 sec) [ -288519.7495] [Alpha ][ 0.900950] . ( 2214 sec) [ -288519.7495] [Topology ] . ( 2295 sec) [ -288477.2142] [Topology ] . ( 2377 sec) [ -288854.2380] [Topology ] . Moving backward . ( 2385 sec) [ -288465.3110] [Topology ] . ( 2466 sec) [ -288461.7968] [Topology ] . ( 2547 sec) [ -288758.9486] [Topology ] . Moving backward . ( 2554 sec) [ -288384.4625] [Topology ] . ( 2635 sec) [ -288495.3889] [Topology ] . Moving backward . ( 2642 sec) [ -288238.0789] [Topology ] . ( 2722 sec) [ -288181.8716] [Topology ] . ( 2846 sec) [ -288335.1226] [GTR parameters ] . ( 2855 sec) [ -288334.8835] [Alpha ][ 0.893415] . ( 2858 sec) [ -288334.8835] [Topology ] . ( 2939 sec) [ -288200.7085] [Topology ] . ( 3022 sec) [ -288503.9614] [Topology ] . Moving backward . ( 3028 sec) [ -288195.0219] [Topology ] . ( 3109 sec) [ -288067.5618] [Topology ] . ( 3190 sec) [ -288288.2585] [Topology ] . Moving backward . ( 3198 sec) [ -288022.2265] [Topology ] . ( 3278 sec) [ -287999.4287] [Topology ] . ( 3359 sec) [ -288171.5224] [Topology ] . Moving backward . ( 3366 sec) [ -287918.3430] [Topology ] . ( 3523 sec) [ -287912.0899] [GTR parameters ] . ( 3531 sec) [ -287910.8707] [Alpha ][ 0.910328] . ( 3534 sec) [ -287910.8707] [Topology ] . ( 3614 sec) [ -288072.8478] [Topology ] . Moving backward . ( 3621 sec) [ -287856.8107] [Topology ] . ( 3703 sec) [ -287946.4966] [Topology ] . Moving backward . ( 3710 sec) [ -287740.7049] [Topology ] . ( 3789 sec) [ -287686.5488] [Topology ] . ( 3870 sec) [ -287645.5212] [Topology ] . ( 3950 sec) [ -287685.1010] [Topology ] . Moving backward . ( 3957 sec) [ -287578.5873] [Topology ] . ( 4037 sec) [ -287643.6377] [Topology ] . Moving backward . ( 4136 sec) [ -287538.3958] [GTR parameters ] . ( 4144 sec) [ -287538.3863] [Alpha ][ 0.908770] . ( 4146 sec) [ -287538.3863] [Topology ] . ( 4225 sec) [ -287594.6322] [Topology ] . Moving backward . ( 4233 sec) [ -287530.7538] [Topology ] . ( 4313 sec) [ -287532.7036] [Topology ] . Moving backward . ( 4320 sec) [ -287497.1937] [Topology ] . ( 4399 sec) [ -287456.1000] [Topology ] . ( 4478 sec) [ -287427.7503] [Topology ] . ( 4557 sec) [ -287348.4917] [Topology ] . ( 4638 sec) [ -287363.6823] [Topology ] . Moving backward . ( 4645 sec) [ -287294.1146] [Topology ] . ( 4809 sec) [ -287251.8843] [GTR parameters ] . ( 4817 sec) [ -287251.8843] [Alpha ][ 0.908770] . ( 4820 sec) [ -287251.8843] [Topology ] . ( 4899 sec) [ -287171.5487] [Topology ] . ( 4978 sec) [ -287086.1294] [Topology ] . ( 5059 sec) [ -287077.6719] [Topology ] . ( 5139 sec) [ -287171.9794] [Topology ] . Moving backward . ( 5146 sec) [ -287031.8247] [Topology ] . ( 5226 sec) [ -287001.2958] [Topology ] . ( 5306 sec) [ -287117.4760] [Topology ] . Moving backward . ( 5313 sec) [ -286974.2777] [Topology ] . ( 5393 sec) [ -287012.0754] [Topology ] . Moving backward . ( 5418 sec) [ -286911.2978] [GTR parameters ] . ( 5426 sec) [ -286911.2877] [Alpha ][ 0.907149] . ( 5429 sec) [ -286911.2877] [Topology ] . ( 5508 sec) [ -286896.7078] [Topology ] . ( 5588 sec) [ -286871.8809] [Topology ] . ( 5667 sec) [ -286984.7044] [Topology ] . Moving backward . ( 5674 sec) [ -286811.2740] [Topology ] . ( 5754 sec) [ -286818.1044] [Topology ] . Moving backward . ( 5761 sec) [ -286785.3860] [Topology ] . ( 5839 sec) [ -286769.3677] [Topology ] . ( 5918 sec) [ -286750.5818] [Topology ] . ( 5997 sec) [ -286723.6189] [Topology ] . ( 6163 sec) [ -286708.7180] [GTR parameters ] . ( 6173 sec) [ -286708.6584] [Alpha ][ 0.903246] . ( 6176 sec) [ -286708.6584] [Topology ] . ( 6255 sec) [ -286784.3772] [Topology ] . Moving backward . ( 6262 sec) [ -286689.7739] [Topology ] . ( 6341 sec) [ -286702.1439] [Topology ] . Moving backward . ( 6348 sec) [ -286676.3812] [Topology ] . ( 6426 sec) [ -286672.9457] [Topology ] . ( 6505 sec) [ -286670.3506] [Topology ] . ( 6583 sec) [ -286662.0464] [Topology ] . ( 6663 sec) [ -286658.0842] [Topology ] . ( 6741 sec) [ -286667.2190] [Topology ] . Moving backward . ( 6778 sec) [ -286643.0525] [GTR parameters ] . ( 6787 sec) [ -286643.0251] [Alpha ][ 0.905796] . ( 6790 sec) [ -286643.0251] [Topology ] . ( 6869 sec) [ -286636.2110] [Topology ] . ( 6947 sec) [ -286623.5690] [Topology ] . ( 7026 sec) [ -286623.8457] [Topology ] . Moving backward . ( 7032 sec) [ -286615.0083] [Topology ] . ( 7111 sec) [ -286613.7891] [Topology ] . ( 7189 sec) [ -286611.7735] [Topology ] . ( 7267 sec) [ -286610.8516] [Topology ] . ( 7345 sec) [ -286610.6227] [Topology ] . ( 7423 sec) [ -286610.5832] [Topology ] . Checking for NNIs, optimizing five branches... . ( 8322 sec) [ -286597.4275] [Topology ] . ( 8343 sec) [ -286597.4189] [GTR parameters ] . ( 8351 sec) [ -286597.4091] [Alpha ][ 0.907303] . ( 8354 sec) [ -286597.4091] [Topology ] . ( 8432 sec) [ -286594.3737] [Topology ] . ( 8511 sec) [ -286587.6398] [Topology ] . ( 8589 sec) [ -286585.2423] [Topology ] . ( 8667 sec) [ -286576.3677] [Topology ] . ( 8745 sec) [ -286574.7172] [Topology ] . ( 8823 sec) [ -286573.5115] [Topology ] . ( 8902 sec) [ -286564.0585] [Topology ] . ( 8981 sec) [ -286538.9315] [Topology ] . ( 9060 sec) [ -286428.3844] [Topology ] . ( 9225 sec) [ -286389.6277] [GTR parameters ] . ( 9234 sec) [ -286389.5327] [Alpha ][ 0.902370] . ( 9237 sec) [ -286389.5327] [Topology ] . ( 9318 sec) [ -286394.7472] [Topology ] . Moving backward . ( 9324 sec) [ -286332.7448] [Topology ] . ( 9403 sec) [ -286321.6744] [Topology ] . ( 9482 sec) [ -286265.6008] [Topology ] . ( 9561 sec) [ -286235.1755] [Topology ] . ( 9639 sec) [ -286181.2017] [Topology ] . ( 9719 sec) [ -286150.7639] [Topology ] . ( 9798 sec) [ -286135.7690] [Topology ] . ( 9878 sec) [ -286140.8034] [Topology ] . Moving backward . ( 9971 sec) [ -286100.0834] [GTR parameters ] . ( 9980 sec) [ -286100.0662] [Alpha ][ 0.904391] . ( 9983 sec) [ -286100.0662] [Topology ] . (10061 sec) [ -286081.4558] [Topology ] . (10140 sec) [ -286075.5899] [Topology ] . (10218 sec) [ -286049.6881] [Topology ] . (10297 sec) [ -286041.1438] [Topology ] . (10376 sec) [ -286008.2394] [Topology ] . (10454 sec) [ -286007.5646] [Topology ] . (10533 sec) [ -286010.5276] [Topology ] . Moving backward . (10540 sec) [ -285993.0302] [Topology ] . (10618 sec) [ -285991.9967] [Topology ] . Checking for NNIs, optimizing five branches... . (11504 sec) [ -285985.4428] [Topology ] . (11583 sec) [ -285985.4066] [GTR parameters ] . (11592 sec) [ -285985.3769] [Alpha ][ 0.907041] . (11595 sec) [ -285985.3769] [Topology ] . (11673 sec) [ -285982.5297] [Topology ] . (11751 sec) [ -285982.5341] [Topology ] . Moving backward . (11758 sec) [ -285979.3161] [Topology ] . (11836 sec) [ -285978.6980] [Topology ] . (11914 sec) [ -285978.4334] [Topology ] . (11992 sec) [ -285977.9093] [Topology ] . (12070 sec) [ -285977.1972] [Topology ] . (12149 sec) [ -285977.1747] [Topology ] . (12227 sec) [ -285977.2990] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . (13034 sec) [ -285968.2407] [Topology ] . (13068 sec) [ -285968.2372] [GTR parameters ] . (13076 sec) [ -285968.2371] [Alpha ][ 0.907948] . (13079 sec) [ -285968.2371] [Topology ] . (13157 sec) [ -285959.6786] [Topology ] . (13235 sec) [ -285925.0799] [Topology ] . (13314 sec) [ -285891.0721] [Topology ] . (13392 sec) [ -285856.0903] [Topology ] . (13471 sec) [ -285788.7991] [Topology ] . (13549 sec) [ -285778.4576] [Topology ] . (13628 sec) [ -285776.3338] [Topology ] . (13708 sec) [ -285776.5744] [Topology ] . Moving backward . (13714 sec) [ -285759.1193] [Topology ] . Checking for NNIs, optimizing five branches... . (14602 sec) [ -285747.0764] [Topology ] . (14697 sec) [ -285747.0203] [GTR parameters ] . (14707 sec) [ -285746.9933] [Alpha ][ 0.905319] . (14710 sec) [ -285746.9933] [Topology ] . (14788 sec) [ -285746.7968] [Topology ] . (14866 sec) [ -285746.7369] [Topology ] . (14944 sec) [ -285746.7296] [Topology ] . (15023 sec) [ -285746.7520] [Topology ] . Moving backward . (15030 sec) [ -285746.5762] [Topology ] . (15108 sec) [ -285746.5615] [Topology ] . (15186 sec) [ -285746.5532] [Topology ] . Checking for NNIs, optimizing five branches... . (15984 sec) [ -285733.3826] [Topology ] . (16005 sec) [ -285733.3816] [GTR parameters ] . (16013 sec) [ -285733.3816] [Alpha ][ 0.905319] . (16016 sec) [ -285733.3816] [Topology ] . (16094 sec) [ -285732.2366] [Topology ] . (16172 sec) [ -285723.1288] [Topology ] . (16251 sec) [ -285699.1891] [Topology ] . (16329 sec) [ -285666.6173] [Topology ] . (16408 sec) [ -285643.2155] [Topology ] . (16486 sec) [ -285629.5330] [Topology ] . (16564 sec) [ -285625.5702] [Topology ] . (16643 sec) [ -285625.0909] [Topology ] . (16721 sec) [ -285625.6961] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . (17528 sec) [ -285596.9494] [Topology ] . (17561 sec) [ -285596.9411] [GTR parameters ] . (17569 sec) [ -285596.9411] [Alpha ][ 0.905319] . (17572 sec) [ -285596.9411] [Topology ] . (17650 sec) [ -285596.4836] [Topology ] . (17728 sec) [ -285594.8929] [Topology ] . (17807 sec) [ -285594.4586] [Topology ] . (17885 sec) [ -285594.2683] [Topology ] . (17963 sec) [ -285594.1722] [Topology ] . (18041 sec) [ -285594.1076] [Topology ] . (18119 sec) [ -285593.9728] [Topology ] . (18197 sec) [ -285593.9676] [Topology ] . (18275 sec) [ -285594.0208] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . (19085 sec) [ -285588.5735] [Topology ] . (19173 sec) [ -285588.5699] [GTR parameters ] . (19181 sec) [ -285588.5642] [Alpha ][ 0.906457] . (19184 sec) [ -285588.5642] [Topology ] . (19262 sec) [ -285588.4962] [Topology ] . (19340 sec) [ -285588.4721] [Topology ] . (19418 sec) [ -285588.4614] [Topology ] . (19496 sec) [ -285588.4585] [Topology ] . (19575 sec) [ -285588.4082] [Topology ] . (19653 sec) [ -285587.7683] [Topology ] . (19731 sec) [ -285586.9778] [Topology ] . (19809 sec) [ -285585.9587] [Topology ] . (19887 sec) [ -285586.0838] [Topology ] . Moving backward . (19912 sec) [ -285585.4213] [GTR parameters ] . (19920 sec) [ -285585.4213] [Alpha ][ 0.906457] . (19923 sec) [ -285585.4213] [Topology ] . (20001 sec) [ -285585.0411] [Topology ] . (20079 sec) [ -285584.8437] [Topology ] . (20158 sec) [ -285584.7255] [Topology ] . (20236 sec) [ -285584.6514] [Topology ] . (20314 sec) [ -285584.6045] [Topology ] . (20392 sec) [ -285584.5758] [Topology ] . Checking for NNIs, optimizing five branches... . (21184 sec) [ -285582.8090] [Topology ] . (21206 sec) [ -285582.8087] [GTR parameters ] . (21214 sec) [ -285582.8087] [Alpha ][ 0.906457] . (21217 sec) [ -285582.8087] [Topology ] . (21295 sec) [ -285581.0857] [Topology ] . (21373 sec) [ -285573.4377] [Topology ] . (21451 sec) [ -285537.1476] [Topology ] . (21529 sec) [ -285518.9264] [Topology ] . (21608 sec) [ -285510.2225] [Topology ] . (21686 sec) [ -285508.4132] [Topology ] . (21764 sec) [ -285507.1256] [Topology ] . (21843 sec) [ -285510.4491] [Topology ] . Moving backward . (21850 sec) [ -285491.9631] [Topology ] . Checking for NNIs, optimizing five branches... . (22726 sec) [ -285488.8440] [Topology ] . (22760 sec) [ -285488.8141] [GTR parameters ] . (22768 sec) [ -285488.8141] [Alpha ][ 0.906457] . (22770 sec) [ -285488.8141] [Topology ] . (22849 sec) [ -285488.1478] [Topology ] . (22927 sec) [ -285487.1893] [Topology ] . (23005 sec) [ -285486.8470] [Topology ] . (23083 sec) [ -285486.6507] [Topology ] . (23162 sec) [ -285486.5444] [Topology ] . (23240 sec) [ -285486.4885] [Topology ] . (23318 sec) [ -285486.4685] [Topology ] . Checking for NNIs, optimizing five branches... . (24122 sec) [ -285485.8175] [Topology ] . (24143 sec) [ -285485.8167] [GTR parameters ] . (24151 sec) [ -285485.8167] [Alpha ][ 0.906457] . (24154 sec) [ -285485.8167] [Topology ] . (24233 sec) [ -285485.7834] [Topology ] . (24311 sec) [ -285485.7979] [Topology ] . Moving backward . (24318 sec) [ -285485.5774] [Topology ] . (24396 sec) [ -285485.5591] [Topology ] . (24474 sec) [ -285485.5493] [Topology ] . (24552 sec) [ -285485.5040] [Topology ] . (24630 sec) [ -285485.2935] [Topology ] . (24709 sec) [ -285485.2510] [Topology ] . (24787 sec) [ -285485.2400] [Topology ] . Checking for NNIs, optimizing five branches... . (25660 sec) [ -285482.8377] [Topology ] . (25682 sec) [ -285482.8364] [GTR parameters ] . (25690 sec) [ -285482.8352] [Alpha ][ 0.907364] . (25693 sec) [ -285482.8352] [Topology ] . (25771 sec) [ -285477.1756] [Topology ] . (25849 sec) [ -285470.6326] [Topology ] . (25927 sec) [ -285463.8033] [Topology ] . (26005 sec) [ -285460.0389] [Topology ] . (26083 sec) [ -285459.4411] [Topology ] . (26162 sec) [ -285459.2983] [Topology ] . (26240 sec) [ -285459.2834] [Topology ] . (26318 sec) [ -285459.3216] [Topology ] . Moving backward . (26325 sec) [ -285459.0846] [Topology ] . Checking for NNIs, optimizing five branches... . (27203 sec) [ -285458.9482] [Topology ] . (27224 sec) [ -285458.9477] [GTR parameters ] . (27232 sec) [ -285458.9477] [Alpha ][ 0.907364] . (27235 sec) [ -285458.9477] [Topology ] . (27314 sec) [ -285458.9403] [Topology ] . (27392 sec) [ -285458.9378] [Topology ] . (27470 sec) [ -285458.9370] [Topology ] . Checking for NNIs, optimizing five branches... . (28265 sec) [ -285458.8273] [Topology ] . (28286 sec) [ -285458.8263] [GTR parameters ] . (28294 sec) [ -285458.8263] [Alpha ][ 0.907364] . (28297 sec) [ -285458.8263] [Topology ] . (28375 sec) [ -285452.7862] [Topology ] . (28453 sec) [ -285447.1007] [Topology ] . (28531 sec) [ -285444.1659] [Topology ] . (28609 sec) [ -285443.5619] [Topology ] . (28687 sec) [ -285443.4754] [Topology ] . (28765 sec) [ -285443.4581] [Topology ] . (28843 sec) [ -285443.4561] [Topology ] . (28921 sec) [ -285443.4595] [Topology ] . Moving backward . (28928 sec) [ -285443.4366] [Topology ] . Checking for NNIs, optimizing five branches... . (29797 sec) [ -285443.2503] [Topology ] . (29831 sec) [ -285443.2414] [GTR parameters ] . (29839 sec) [ -285443.2391] [Alpha ][ 0.906456] . (29842 sec) [ -285443.2391] [Topology ] . (29920 sec) [ -285434.3830] [Topology ] . (29998 sec) [ -285424.8760] [Topology ] . (30076 sec) [ -285423.4180] [Topology ] . (30154 sec) [ -285423.2059] [Topology ] . (30232 sec) [ -285423.2116] [Topology ] . Moving backward . (30239 sec) [ -285422.9648] [Topology ] . (30317 sec) [ -285422.9543] [Topology ] . (30396 sec) [ -285422.9523] [Topology ] . (30474 sec) [ -285422.9525] [Topology ] . Checking for NNIs, optimizing five branches... . (31269 sec) [ -285422.6250] [Topology ] . (31290 sec) [ -285422.6215] [GTR parameters ] . (31298 sec) [ -285422.6215] [Alpha ][ 0.906456] . (31301 sec) [ -285422.6215] [Topology ] . (31379 sec) [ -285422.5595] [Topology ] . (31457 sec) [ -285422.5479] [Topology ] . (31535 sec) [ -285422.5442] [Topology ] . (31614 sec) [ -285422.5430] [Topology ] . (31692 sec) [ -285422.5432] [Topology ] . Checking for NNIs, optimizing five branches... . (32487 sec) [ -285422.5422] [Topology ] . (32508 sec) [ -285422.5421] [GTR parameters ] . (32516 sec) [ -285422.5421] [Alpha ][ 0.906456] . (32519 sec) [ -285422.5421] [Topology ] . (32597 sec) [ -285422.5381] [Topology ] . (32675 sec) [ -285422.5333] [Topology ] . (32753 sec) [ -285422.5308] [Topology ] . (32832 sec) [ -285422.5307] [Topology ] . Checking for NNIs, optimizing five branches... . (33630 sec) [ -285418.6528] [Topology ] . (33651 sec) [ -285418.6523] [GTR parameters ] . (33659 sec) [ -285418.6523] [Alpha ][ 0.906456] . (33662 sec) [ -285418.6523] [Topology ] . (33740 sec) [ -285418.5635] [Topology ] . (33819 sec) [ -285418.5531] [Topology ] . (33897 sec) [ -285418.5590] [Topology ] . Moving backward . (33904 sec) [ -285418.5091] [Topology ] . (33982 sec) [ -285418.5046] [Topology ] . (34061 sec) [ -285418.5026] [Topology ] . (34139 sec) [ -285418.5018] [Topology ] . Checking for NNIs, optimizing five branches... . (34938 sec) [ -285418.3221] [Topology ] . (34959 sec) [ -285418.3204] [GTR parameters ] . (34967 sec) [ -285418.3196] [Alpha ][ 0.907363] . (34970 sec) [ -285418.3196] [Topology ] . (35049 sec) [ -285417.7224] [Topology ] . (35127 sec) [ -285417.6254] [Topology ] . (35205 sec) [ -285417.5920] [Topology ] . (35283 sec) [ -285417.5778] [Topology ] . (35362 sec) [ -285417.5720] [Topology ] . (35440 sec) [ -285417.5707] [Topology ] . Checking for NNIs, optimizing five branches... . (36234 sec) [ -285417.4568] [Topology ] . (36255 sec) [ -285417.4566] [GTR parameters ] . (36263 sec) [ -285417.4566] [Alpha ][ 0.907363] . (36266 sec) [ -285417.4566] [Topology ] . (36344 sec) [ -285417.3350] [Topology ] . (36422 sec) [ -285417.3093] [Topology ] . (36501 sec) [ -285417.3025] [Topology ] . (36579 sec) [ -285417.3201] [Topology ] . Moving backward . (36586 sec) [ -285417.2786] [Topology ] . (36664 sec) [ -285417.2761] [Topology ] . (36743 sec) [ -285417.2566] [Topology ] . (36821 sec) [ -285416.1718] [Topology ] . (36900 sec) [ -285415.8841] [Topology ] . Checking for NNIs, optimizing five branches... . (37767 sec) [ -285414.3327] [Topology ] . (37788 sec) [ -285414.3299] [GTR parameters ] . (37796 sec) [ -285414.3299] [Alpha ][ 0.907363] . (37799 sec) [ -285414.3299] [Topology ] . (37878 sec) [ -285414.0819] [Topology ] . (37956 sec) [ -285414.0302] [Topology ] . (38034 sec) [ -285414.0085] [Topology ] . (38113 sec) [ -285413.9975] [Topology ] . (38191 sec) [ -285413.9915] [Topology ] . (38269 sec) [ -285413.9881] [Topology ] . Checking for NNIs, optimizing five branches... . (39063 sec) [ -285395.1370] [Topology ] . (39096 sec) [ -285395.1240] [GTR parameters ] . (39105 sec) [ -285395.1099] [Alpha ][ 0.905478] . (39108 sec) [ -285395.1099] [Topology ] . (39187 sec) [ -285380.6382] [Topology ] . (39266 sec) [ -285375.0166] [Topology ] . (39344 sec) [ -285357.5360] [Topology ] . (39423 sec) [ -285340.0120] [Topology ] . (39501 sec) [ -285331.5611] [Topology ] . (39580 sec) [ -285322.7689] [Topology ] . (39658 sec) [ -285312.4182] [Topology ] . (39737 sec) [ -285301.6091] [Topology ] . (39816 sec) [ -285299.3745] [Topology ] . (39980 sec) [ -285299.1978] [GTR parameters ] . (39988 sec) [ -285299.1922] [Alpha ][ 0.906583] . (39991 sec) [ -285299.1922] [Topology ] . (40070 sec) [ -285304.8002] [Topology ] . Moving backward . (40077 sec) [ -285288.3131] [Topology ] . (40156 sec) [ -285281.8017] [Topology ] . (40234 sec) [ -285280.1240] [Topology ] . (40313 sec) [ -285279.3907] [Topology ] . (40392 sec) [ -285279.2432] [Topology ] . (40471 sec) [ -285281.8520] [Topology ] . Moving backward . (40477 sec) [ -285277.4587] [Topology ] . (40556 sec) [ -285276.9603] [Topology ] . Checking for NNIs, optimizing five branches... . (41431 sec) [ -285249.4848] [Topology ] . (41453 sec) [ -285249.4837] [GTR parameters ] . (41461 sec) [ -285249.4782] [Alpha ][ 0.907680] . (41464 sec) [ -285249.4782] [Topology ] . (41543 sec) [ -285238.0786] [Topology ] . (41621 sec) [ -285233.1491] [Topology ] . (41700 sec) [ -285230.2155] [Topology ] . (41778 sec) [ -285226.8739] [Topology ] . (41857 sec) [ -285225.5400] [Topology ] . (41935 sec) [ -285224.4200] [Topology ] . (42014 sec) [ -285223.6320] [Topology ] . (42093 sec) [ -285223.5771] [Topology ] . (42172 sec) [ -285223.8297] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . (42976 sec) [ -285212.4328] [Topology ] . (43055 sec) [ -285212.4287] [GTR parameters ] . (43063 sec) [ -285212.4287] [Alpha ][ 0.907680] . (43066 sec) [ -285212.4287] [Topology ] . (43144 sec) [ -285194.2862] [Topology ] . (43223 sec) [ -285181.2634] [Topology ] . (43301 sec) [ -285168.8008] [Topology ] . (43380 sec) [ -285161.6195] [Topology ] . (43458 sec) [ -285160.0064] [Topology ] . (43537 sec) [ -285157.8272] [Topology ] . (43615 sec) [ -285157.2685] [Topology ] . (43694 sec) [ -285157.0442] [Topology ] . (43772 sec) [ -285156.9468] [Topology ] . Checking for NNIs, optimizing five branches... . (44664 sec) [ -285141.6108] [Topology ] . (44697 sec) [ -285141.6019] [GTR parameters ] . (44706 sec) [ -285141.6019] [Alpha ][ 0.907680] . (44708 sec) [ -285141.6019] [Topology ] . (44787 sec) [ -285141.1293] [Topology ] . (44866 sec) [ -285141.0788] [Topology ] . (44944 sec) [ -285141.1503] [Topology ] . Moving backward . (44951 sec) [ -285140.3076] [Topology ] . (45030 sec) [ -285140.2760] [Topology ] . (45108 sec) [ -285140.2616] [Topology ] . (45186 sec) [ -285140.2546] [Topology ] . Checking for NNIs, optimizing five branches... . (45989 sec) [ -285125.3746] [Topology ] . (46022 sec) [ -285125.3732] [GTR parameters ] . (46030 sec) [ -285125.3732] [Alpha ][ 0.907680] . (46033 sec) [ -285125.3732] [Topology ] . (46112 sec) [ -285125.1581] [Topology ] . (46190 sec) [ -285125.1109] [Topology ] . (46269 sec) [ -285125.0977] [Topology ] . (46347 sec) [ -285125.0963] [Topology ] . (46426 sec) [ -285125.0999] [Topology ] . Moving backward . (46433 sec) [ -285125.0736] [Topology ] . (46511 sec) [ -285125.0723] [Topology ] . Checking for NNIs, optimizing five branches... . (47315 sec) [ -285124.2289] [Topology ] . (47336 sec) [ -285124.2286] [GTR parameters ] . (47344 sec) [ -285124.2286] [Alpha ][ 0.907680] . (47347 sec) [ -285124.2286] [Topology ] . (47425 sec) [ -285124.2223] [Topology ] . (47504 sec) [ -285124.2209] [Topology ] . (47582 sec) [ -285124.2205] [Topology ] . Checking for NNIs, optimizing five branches... . (48381 sec) [ -285124.1366] [Topology ] . (48402 sec) [ -285124.1365] [GTR parameters ] . (48410 sec) [ -285124.1365] [Alpha ][ 0.907680] . (48413 sec) [ -285124.1365] [Topology ] . (48492 sec) [ -285124.1066] [Topology ] . (48570 sec) [ -285124.1003] [Topology ] . (48649 sec) [ -285124.0976] [Topology ] . (48727 sec) [ -285124.0963] [Topology ] . (48806 sec) [ -285124.0958] [Topology ] . Checking for NNIs, optimizing five branches... . (49605 sec) [ -285124.0671] [Topology ] . (49626 sec) [ -285124.0671] [GTR parameters ] . (49634 sec) [ -285124.0671] [Alpha ][ 0.907680] . (49637 sec) [ -285124.0671] [Topology ] . (49716 sec) [ -285124.0664] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -285124.066358. . Printing the most likely tree in file 'nucleic_M4055_306x7062_2008.phy_phyml_tree.txt'... . Time used 14h15m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 51344.13user 0.00system 14:15:58elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps