.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2944_80x1495_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . '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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 494 patterns found. (out of a total of 1495 sites) . 1077 sites without polymorphism (72.04%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9243.1584] [Ts/ts ratio ][ 3.683609] . ( 2 sec) [ -9241.0357] [ 1257] [depth= 1] . ( 2 sec) [ -9237.2060] [ 1257] [depth= 1] . ( 2 sec) [ -9234.4655] [ 1254] [depth= 1] . ( 2 sec) [ -9232.3141] [ 1254] [depth= 1] . ( 2 sec) [ -9231.7112] [ 1254] [depth= 1] . ( 3 sec) [ -9228.8010] [ 1253] [depth= 1] . ( 3 sec) [ -9226.2885] [ 1254] [depth= 1] . ( 4 sec) [ -9220.3924] [ 1254] [depth= 1] . ( 4 sec) [ -9219.7964] [ 1253] [depth= 1] . ( 5 sec) [ -9214.2584] [ 1252] [depth= 1] . ( 5 sec) [ -9214.0020] [ 1252] [depth= 1] . ( 5 sec) [ -9213.8592] [ 1253] [depth= 1] . ( 6 sec) [ -9213.4130] [ 1253] [depth= 1] . ( 6 sec) [ -9211.5672] [ 1253] [depth= 1] . ( 7 sec) [ -9209.2421] [ 1253] [depth= 2] . ( 7 sec) [ -9207.6531] [ 1253] [depth= 1] . ( 8 sec) [ -9206.6844] [ 1253] [depth= 1] . ( 8 sec) [ -9206.4873] [ 1253] [depth= 1] . ( 8 sec) [ -9198.9763] [ 1251] [depth= 1] . ( 9 sec) [ -9198.3646] [ 1251] [depth= 1] . ( 9 sec) [ -9197.9460] [ 1252] [depth= 1] . ( 9 sec) [ -9196.2210] [ 1252] [depth= 1] . ( 9 sec) [ -9195.0209] [ 1252] [depth= 1] . ( 9 sec) [ -9191.0126] [ 1251] [depth= 1] . ( 10 sec) [ -9188.9647] [ 1252] [depth= 3] . ( 10 sec) [ -9188.7889] [ 1252] [depth= 1] . ( 10 sec) [ -9187.5907] [ 1252] [depth= 1] . ( 11 sec) [ -9185.6928] [ 1252] [depth= 1] . ( 12 sec) [ -9179.4086] [ 1250] [depth= 1] . ( 12 sec) [ -9179.1363] [ 1250] [depth= 1] . ( 13 sec) [ -9177.4790] [ 1250] [depth= 3] . ( 14 sec) [ -9174.5992] [ 1249] [depth= 1] . ( 15 sec) [ -9171.8028] [ 1248] [depth= 1] . ( 15 sec) [ -9171.3403] [ 1249] [depth= 1] . ( 15 sec) [ -9171.3300] [ 1248] [depth= 1] . ( 16 sec) [ -9171.1413] [ 1248] [depth= 1] . ( 16 sec) [ -9170.7796] [ 1247] [depth= 1] . ( 16 sec) [ -9170.5918] [ 1248] [depth= 1] . ( 16 sec) [ -9170.1423] [ 1249] [depth= 1] . ( 17 sec) [ -9168.7547] [ 1248] [depth= 1] . ( 17 sec) [ -9165.0679] [ 1247] [depth= 1] . ( 18 sec) [ -9153.4696] [ 1247] [depth= 1] . ( 18 sec) [ -9153.2717] [ 1251] [depth= 4] . ( 19 sec) [ -9137.5203] [ 1245] [depth= 4] . ( 20 sec) [ -9137.1988] [ 1246] [depth= 2] . ( 20 sec) [ -9134.5222] [ 1245] [depth= 2] . ( 20 sec) [ -9133.2112] [ 1245] [depth= 1] . ( 21 sec) [ -9133.1913] [ 1245] [depth= 1] . ( 21 sec) [ -9131.0246] [ 1243] [depth= 3] . ( 21 sec) [ -9130.2252] [ 1244] [depth= 2] . ( 21 sec) [ -9126.2848] [ 1243] [depth= 2] . ( 23 sec) [ -9126.1071] [ 1244] [depth= 1] . ( 23 sec) [ -9123.4567] [ 1243] [depth= 2] . ( 24 sec) [ -9122.4178] [ 1242] [depth= 2] . ( 24 sec) [ -9121.3420] [ 1242] [depth= 1] . ( 25 sec) [ -9121.2426] [ 1242] [depth= 2] . ( 25 sec) [ -9120.2571] [ 1241] [depth= 2] . ( 27 sec) [ -9119.8850] [ 1241] [depth= 1] . ( 28 sec) [ -9119.8104] [ 1242] [depth= 1] . ( 30 sec) [ -9059.3714] [Branch lengths ] . ( 30 sec) [ -9059.2673] [Ts/ts ratio ][ 3.785405] . ( 32 sec) [ -9058.3941] [ 1241] [depth= 1] . ( 36 sec) [ -9057.2885] [ 1240] [depth= 1] . ( 39 sec) [ -9057.2625] [ 1240] [depth= 1] . ( 42 sec) [ -9054.1921] [ 1240] [depth= 3] . ( 61 sec) [ -9054.1498] [ 1241] [depth= 3] . ( 65 sec) [ -9054.1059] [ 1241] [depth= 1] . ( 67 sec) [ -9047.7919] [Branch lengths ] . ( 67 sec) [ -9047.7886] [Ts/ts ratio ][ 3.803816] . ( 71 sec) [ -9047.3558] [ 1241] [depth= 1] . ( 73 sec) [ -9047.0624] [ 1241] [depth= 1] . ( 105 sec) [ -9045.3494] [Branch lengths ] . ( 105 sec) [ -9045.3487] [Ts/ts ratio ][ 3.811609] . ( 142 sec) [ -9045.2287] [Branch lengths ] . ( 223 sec) [ -9045.2081] [Branch lengths ] . ( 223 sec) [ -9045.2081] [Topology ] . ( 225 sec) [ -9045.2056] [Topology ] . ( 227 sec) [ -9045.2045] [Topology ] . ( 229 sec) [ -9045.2039] [Topology ] . ( 229 sec) [ -9045.2035] [Ts/ts ratio ][ 3.817355] . ( 229 sec) [ -9045.2035] [Topology ] . ( 231 sec) [ -9045.2031] [Topology ] . ( 231 sec) [ -9045.2031] [Ts/ts ratio ][ 3.817355] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9045.203135. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 97 29.365891 0.951000 0.030100 89 15.759021 0.913000 0.022243 100 153.031309 1.000000 0.065232 57 8.813271 0.858000 0.006912 46 6.333174 0.836000 0.006048 68 38.675290 0.975000 0.012487 17 2.169331 0.698000 0.001889 70 31.379461 0.970000 0.009176 24 7.638090 0.824000 0.003473 59 12.725970 0.875000 0.005472 93 30.652138 0.951000 0.007651 36 -1.000000 0.000000 0.000000 99 40.165373 0.980000 0.007494 81 4.054095 0.731000 0.001444 44 5.348058 0.694000 0.003325 19 19.828656 0.927000 0.005926 4 -1.000000 0.000000 0.000000 47 14.367069 0.888000 0.004670 31 7.428848 0.877000 0.006184 57 5.740488 0.698000 0.003112 73 12.030405 0.751000 0.006276 43 18.009519 0.898000 0.007062 90 45.948671 0.978000 0.011394 99 36.175850 0.972000 0.015105 68 7.229702 0.627000 0.007539 68 26.851369 0.968000 0.013778 7 -1.000000 0.000000 0.000000 45 46.412286 0.990000 0.010197 37 3.225358 0.712000 0.001639 60 17.780418 0.944000 0.004521 98 31.389215 0.943000 0.007181 51 0.767707 0.139000 0.001483 48 2.236731 0.754000 0.001332 10 6.633469 0.816000 0.003434 100 65.989918 0.995000 0.020780 98 12.597166 0.915000 0.012960 12 0.616019 0.252000 0.002073 100 89.037308 0.999000 0.028653 100 101.035734 1.000000 0.032219 40 1.778198 0.740000 0.002156 48 2.152574 0.702000 0.001677 94 34.765239 0.964000 0.013998 57 4.899711 0.714000 0.002808 67 44.699152 0.974000 0.009170 31 -1.000000 0.000000 0.000000 91 11.408316 0.826000 0.007209 97 44.161186 0.979000 0.016461 100 91.351674 0.999000 0.028450 100 91.365545 0.999000 0.027663 98 15.466797 0.904000 0.004456 64 14.943394 0.911000 0.009078 81 23.969225 0.957000 0.013654 100 126.846775 1.000000 0.036777 97 20.841088 0.939000 0.009099 50 5.020898 0.736000 0.003536 91 20.973160 0.923000 0.007875 46 0.891605 0.173000 0.004275 81 26.185082 0.960000 0.012297 100 70.158631 1.000000 0.023443 50 11.556015 0.889000 0.005625 1 4.417027 0.745000 0.001455 28 10.712147 0.859000 0.003061 35 4.326387 0.472000 0.003024 3 7.005551 0.755000 0.001500 35 12.754910 0.871000 0.005055 100 70.375169 0.994000 0.016906 55 3.132316 0.441000 0.004306 2 5.549852 0.782000 0.001479 1 -1.000000 0.000000 0.000000 1 9.212235 0.791000 0.001887 25 6.573024 0.627000 0.004344 33 0.633543 0.090000 0.003567 2 -1.000000 0.000000 0.000000 92 39.665136 0.996000 0.020652 5 1.288069 0.377000 0.001476 94 38.110300 0.988000 0.014466 33 5.218625 0.538000 0.004793 . Printing the most likely tree in file 'nucleic_M2944_80x1495_2006.phy_phyml_tree.txt'... . Time used 5h16m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo