.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2932_68x1712_2006.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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 1264 patterns found. (out of a total of 1712 sites) . 601 sites without polymorphism (35.11%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 45Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -15465.7212] [GTR parameters ] . ( 8 sec) [ -15431.9484] [Alpha ][ 0.613860] . ( 8 sec) [ -15431.3316] [ 3250] [depth= 1] . ( 8 sec) [ -15419.5075] [ 3256] [depth= 2] . ( 12 sec) [ -15411.1590] [ 3252] [depth= 2] . ( 23 sec) [ -15408.6623] [ 3258] [depth= 1] . ( 23 sec) [ -15408.0005] [ 3252] [depth= 1] . ( 34 sec) [ -15400.9527] [ 3250] [depth= 1] . ( 34 sec) [ -15397.3366] [ 3252] [depth= 1] . ( 34 sec) [ -15376.3843] [ 3277] [depth= 1] . ( 40 sec) [ -15374.4606] [ 3285] [depth= 2] . ( 49 sec) [ -15373.9655] [ 3263] [depth= 2] . ( 49 sec) [ -15355.4343] [ 3262] [depth= 3] . ( 50 sec) [ -15351.9127] [ 3264] [depth= 2] . ( 53 sec) [ -15344.9376] [ 3265] [depth= 1] . ( 53 sec) [ -15326.9652] [ 3261] [depth= 1] . ( 53 sec) [ -15326.5255] [ 3261] [depth= 1] . ( 65 sec) [ -15321.7840] [ 3261] [depth= 1] . ( 65 sec) [ -15312.3406] [ 3261] [depth= 1] . ( 65 sec) [ -15307.4000] [ 3261] [depth= 2] . ( 65 sec) [ -15277.8484] [ 3234] [depth= 2] . ( 68 sec) [ -15276.4217] [ 3234] [depth= 1] . ( 69 sec) [ -15202.4133] [ 3227] [depth= 2] . ( 69 sec) [ -15199.4182] [ 3227] [depth= 1] . ( 77 sec) [ -15195.2629] [ 3230] [depth= 1] . ( 80 sec) [ -15187.9551] [ 3247] [depth= 1] . ( 80 sec) [ -15184.9463] [ 3245] [depth= 1] . ( 91 sec) [ -15181.9493] [ 3240] [depth= 1] . ( 91 sec) [ -15173.7293] [ 3240] [depth= 1] . ( 92 sec) [ -15159.5651] [ 3243] [depth= 1] . ( 92 sec) [ -15156.0327] [ 3236] [depth= 2] . ( 92 sec) [ -15152.8286] [ 3249] [depth= 1] . ( 92 sec) [ -15152.2134] [ 3249] [depth= 1] . ( 93 sec) [ -15151.3561] [ 3249] [depth= 1] . ( 93 sec) [ -15151.3274] [ 3249] [depth= 5] . ( 93 sec) [ -15149.1404] [ 3249] [depth= 7] . ( 97 sec) [ -15144.8066] [ 3248] [depth= 5] . ( 97 sec) [ -15143.2705] [ 3248] [depth= 3] . ( 97 sec) [ -15133.7937] [ 3248] [depth= 1] . ( 97 sec) [ -15126.5949] [ 3247] [depth= 1] . ( 98 sec) [ -15124.2916] [ 3248] [depth= 3] . ( 98 sec) [ -15123.9395] [ 3248] [depth= 2] . ( 101 sec) [ -15120.4692] [ 3248] [depth= 2] . ( 102 sec) [ -15118.2524] [ 3249] [depth= 2] . ( 102 sec) [ -15116.8383] [ 3249] [depth= 1] . ( 103 sec) [ -15112.7125] [ 3249] [depth= 2] . ( 103 sec) [ -15112.4351] [ 3249] [depth= 5] . ( 110 sec) [ -15112.0208] [ 3249] [depth= 4] . ( 110 sec) [ -15111.5101] [ 3249] [depth= 1] . ( 111 sec) [ -15104.8624] [ 3253] [depth= 1] . ( 111 sec) [ -15104.1956] [ 3251] [depth= 6] . ( 111 sec) [ -15103.6662] [ 3252] [depth= 1] . ( 119 sec) [ -15100.2220] [ 3258] [depth= 2] . ( 138 sec) [ -15100.0920] [ 3259] [depth= 1] . ( 149 sec) [ -15097.1398] [ 3259] [depth= 1] . ( 149 sec) [ -15096.4741] [ 3258] [depth= 1] . ( 162 sec) [ -15094.3465] [ 3258] [depth= 1] . ( 166 sec) [ -15094.0593] [ 3259] [depth= 1] . ( 166 sec) [ -15090.2902] [ 3249] [depth= 1] . ( 166 sec) [ -15080.2999] [ 3238] [depth= 2] . ( 166 sec) [ -15080.2358] [ 3239] [depth= 1] . ( 203 sec) [ -15079.9723] [ 3239] [depth= 2] . ( 203 sec) [ -15079.5835] [ 3239] [depth= 1] . ( 214 sec) [ -15076.1749] [ 3239] [depth= 1] . ( 215 sec) [ -15075.1887] [ 3238] [depth= 2] . ( 215 sec) [ -15069.9584] [ 3237] [depth= 4] . ( 215 sec) [ -15069.8993] [ 3237] [depth= 2] . ( 219 sec) [ -15069.8892] [ 3237] [depth= 3] . ( 219 sec) [ -15069.6948] [ 3237] [depth= 1] . ( 220 sec) [ -15069.4165] [ 3237] [depth= 1] . ( 223 sec) [ -15069.3722] [ 3237] [depth= 3] . ( 226 sec) [ -15069.3104] [ 3237] [depth= 2] . ( 226 sec) [ -15069.1081] [ 3237] [depth= 1] . ( 227 sec) [ -15068.8729] [ 3237] [depth= 2] . ( 233 sec) [ -15068.8201] [ 3237] [depth= 1] . ( 234 sec) [ -15068.8012] [ 3237] [depth= 1] . ( 234 sec) [ -15068.7635] [ 3237] [depth= 3] . ( 238 sec) [ -15068.7401] [ 3237] [depth= 1] . ( 239 sec) [ -15068.7290] [ 3237] [depth= 4] . ( 239 sec) [ -15068.6621] [ 3237] [depth= 4] . ( 239 sec) [ -15068.6278] [ 3237] [depth= 1] . ( 239 sec) [ -15068.5967] [ 3237] [depth= 4] . ( 244 sec) [ -14994.9087] [Branch lengths ] . ( 253 sec) [ -14981.2253] [GTR parameters ] . ( 253 sec) [ -14981.1804] [Alpha ][ 0.604476] . ( 254 sec) [ -14978.9723] [ 3236] [depth= 1] . ( 254 sec) [ -14976.6067] [ 3230] [depth= 3] . ( 257 sec) [ -14972.2968] [ 3222] [depth= 3] . ( 285 sec) [ -14971.7749] [ 3219] [depth= 1] . ( 307 sec) [ -14971.7620] [ 3223] [depth= 1] . ( 314 sec) [ -14971.7068] [ 3223] [depth= 2] . ( 315 sec) [ -14971.6709] [ 3223] [depth= 1] . ( 315 sec) [ -14971.6461] [ 3223] [depth= 1] . ( 326 sec) [ -14971.6271] [ 3223] [depth= 1] . ( 329 sec) [ -14971.3515] [ 3223] [depth= 1] . ( 329 sec) [ -14971.0514] [ 3223] [depth= 1] . ( 335 sec) [ -14964.3127] [ 3216] [depth= 2] . ( 336 sec) [ -14963.8229] [ 3216] [depth= 1] . ( 346 sec) [ -14963.1115] [ 3215] [depth= 1] . ( 347 sec) [ -14963.0868] [ 3193] [depth= 1] . ( 350 sec) [ -14960.3639] [ 3216] [depth= 1] . ( 354 sec) [ -14958.9902] [ 3215] [depth= 1] . ( 365 sec) [ -14958.8172] [ 3216] [depth= 2] . ( 385 sec) [ -14958.8010] [ 3216] [depth= 1] . ( 427 sec) [ -14957.8966] [ 3220] [depth= 2] . ( 428 sec) [ -14957.7788] [ 3215] [depth= 2] . ( 431 sec) [ -14955.8611] [ 3223] [depth= 1] . ( 471 sec) [ -14952.8580] [ 3223] [depth= 1] . ( 473 sec) [ -14952.3391] [ 3223] [depth= 1] . ( 548 sec) [ -14952.2418] [ 3223] [depth= 1] . ( 613 sec) [ -14937.8204] [Branch lengths ] . ( 618 sec) [ -14937.0827] [GTR parameters ] . ( 619 sec) [ -14936.9047] [Alpha ][ 0.587370] . ( 619 sec) [ -14936.1405] [ 3219] [depth= 1] . ( 707 sec) [ -14936.0986] [ 3219] [depth= 1] . ( 757 sec) [ -14934.7871] [ 3224] [depth= 3] . ( 761 sec) [ -14934.6800] [ 3224] [depth= 3] . ( 773 sec) [ -14934.6669] [ 3224] [depth= 1] . ( 792 sec) [ -14933.9449] [ 3224] [depth= 2] . ( 793 sec) [ -14933.0960] [ 3224] [depth= 4] . ( 798 sec) [ -14933.0026] [ 3224] [depth= 3] . ( 815 sec) [ -14932.6995] [ 3224] [depth= 1] . ( 1009 sec) [ -14929.6453] [Branch lengths ] . ( 1013 sec) [ -14929.5911] [GTR parameters ] . ( 1014 sec) [ -14929.5232] [Alpha ][ 0.576806] . ( 1169 sec) [ -14929.4611] [ 3224] [depth= 4] . ( 1417 sec) [ -14928.9039] [Branch lengths ] . ( 1421 sec) [ -14928.8892] [GTR parameters ] . ( 1421 sec) [ -14928.8692] [Alpha ][ 0.571169] . ( 1566 sec) [ -14928.7488] [Branch lengths ] . ( 1566 sec) [ -14928.7488] [Topology ] . ( 1569 sec) [ -14928.6881] [Topology ] . ( 1573 sec) [ -14928.3742] [Topology ] . ( 1576 sec) [ -14926.6987] [Topology ] . ( 1580 sec) [ -14922.8450] [Topology ] . ( 1583 sec) [ -14921.8662] [Topology ] . ( 1586 sec) [ -14921.6536] [Topology ] . ( 1591 sec) [ -14921.6495] [GTR parameters ] . ( 1591 sec) [ -14921.6433] [Alpha ][ 0.568024] . ( 1591 sec) [ -14921.6433] [Topology ] . ( 1595 sec) [ -14921.5480] [Topology ] . ( 1598 sec) [ -14921.4933] [Topology ] . ( 1602 sec) [ -14921.4613] [Topology ] . ( 1605 sec) [ -14921.4424] [Topology ] . ( 1608 sec) [ -14921.4314] [Topology ] . ( 1612 sec) [ -14921.4251] [Topology ] . ( 1615 sec) [ -14921.4246] [GTR parameters ] . ( 1615 sec) [ -14921.4244] [Alpha ][ 0.567456] . ( 1615 sec) [ -14921.4244] [Topology ] . ( 1619 sec) [ -14921.4204] [Topology ] . ( 1622 sec) [ -14921.4180] [Topology ] . ( 1626 sec) [ -14921.4165] [Topology ] . ( 1629 sec) [ -14921.4156] [Topology ] . ( 1631 sec) [ -14921.4155] [GTR parameters ] . ( 1631 sec) [ -14921.4155] [Alpha ][ 0.567456] . ( 1631 sec) [ -14921.4155] [Topology ] . ( 1635 sec) [ -14921.4148] [Topology ] . ( 1636 sec) [ -14921.4148] [GTR parameters ] . ( 1636 sec) [ -14921.4148] [Alpha ][ 0.567456] . Checking for NNIs, optimizing five branches... . ( 1667 sec) [ -14921.3108] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1697 sec) [ -14921.3107] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1728 sec) [ -14921.3086] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14921.308572. . Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'... . Time used 0h29m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1748.20user 0.00system 29:19.82elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps