.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2716_79x1252_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 . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 280 patterns found. (out of a total of 1252 sites) . 984 sites without polymorphism (78.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3425.3703] [Ts/ts ratio ][ 2.500003] . ( 0 sec) [ -3424.9966] [ 336] [depth= 1] . ( 0 sec) [ -3424.9207] [ 336] [depth= 1] . ( 1 sec) [ -3422.8037] [ 336] [depth= 1] . ( 1 sec) [ -3422.4441] [ 336] [depth= 1] . ( 1 sec) [ -3421.3838] [ 336] [depth= 1] . ( 1 sec) [ -3421.3225] [ 336] [depth= 1] . ( 1 sec) [ -3421.3048] [ 336] [depth= 2] . ( 2 sec) [ -3421.2861] [ 336] [depth= 2] . ( 2 sec) [ -3421.1313] [ 336] [depth= 2] . ( 2 sec) [ -3420.9183] [ 336] [depth= 3] . ( 3 sec) [ -3420.8684] [ 336] [depth= 1] . ( 3 sec) [ -3420.5529] [ 336] [depth= 1] . ( 3 sec) [ -3420.3194] [ 336] [depth= 1] . ( 3 sec) [ -3420.2889] [ 336] [depth= 3] . ( 3 sec) [ -3418.6332] [ 336] [depth= 8] . ( 3 sec) [ -3414.2657] [ 335] [depth= 8] . ( 4 sec) [ -3414.1174] [ 335] [depth= 1] . ( 4 sec) [ -3410.9256] [ 338] [depth= 1] . ( 4 sec) [ -3410.6699] [ 339] [depth= 1] . ( 5 sec) [ -3410.5958] [ 339] [depth= 2] . ( 6 sec) [ -3409.5902] [ 339] [depth= 1] . ( 7 sec) [ -3408.6018] [ 339] [depth= 1] . ( 8 sec) [ -3408.5680] [ 339] [depth= 2] . ( 8 sec) [ -3408.5421] [ 339] [depth= 1] . ( 8 sec) [ -3408.5145] [ 339] [depth= 3] . ( 8 sec) [ -3408.2566] [ 339] [depth= 1] . ( 9 sec) [ -3408.1944] [ 339] [depth= 2] . ( 9 sec) [ -3408.1483] [ 339] [depth= 7] . ( 9 sec) [ -3408.0380] [ 339] [depth= 2] . ( 9 sec) [ -3407.9728] [ 339] [depth= 1] . ( 9 sec) [ -3407.8684] [ 339] [depth= 7] . ( 9 sec) [ -3407.6678] [ 339] [depth= 5] . ( 9 sec) [ -3407.6343] [ 339] [depth= 1] . ( 10 sec) [ -3407.0643] [ 339] [depth= 1] . ( 10 sec) [ -3407.0520] [ 339] [depth= 4] . ( 10 sec) [ -3406.6689] [ 339] [depth= 1] . ( 10 sec) [ -3406.6559] [ 339] [depth= 2] . ( 11 sec) [ -3406.6440] [ 339] [depth= 2] . ( 12 sec) [ -3406.5560] [ 338] [depth= 1] . ( 12 sec) [ -3395.5941] [ 337] [depth= 3] . ( 12 sec) [ -3394.9370] [ 337] [depth= 1] . ( 13 sec) [ -3392.7550] [ 337] [depth= 2] . ( 13 sec) [ -3391.4333] [ 336] [depth= 1] . ( 13 sec) [ -3388.7268] [ 331] [depth= 2] . ( 13 sec) [ -3385.6970] [ 331] [depth= 1] . ( 14 sec) [ -3385.5948] [ 331] [depth= 1] . ( 14 sec) [ -3384.8437] [ 331] [depth= 1] . ( 14 sec) [ -3384.0527] [ 331] [depth= 1] . ( 14 sec) [ -3383.9523] [ 332] [depth= 3] . ( 15 sec) [ -3383.9383] [ 332] [depth= 2] . ( 15 sec) [ -3383.8583] [ 332] [depth= 1] . ( 15 sec) [ -3383.4566] [ 332] [depth= 4] . ( 15 sec) [ -3383.2147] [ 332] [depth= 1] . ( 16 sec) [ -3382.6170] [ 332] [depth= 2] . ( 16 sec) [ -3381.3541] [ 332] [depth= 4] . ( 16 sec) [ -3380.7750] [ 332] [depth= 1] . ( 16 sec) [ -3380.5315] [ 332] [depth= 1] . ( 16 sec) [ -3380.2680] [ 332] [depth= 2] . ( 16 sec) [ -3380.0826] [ 332] [depth= 4] . ( 16 sec) [ -3379.8569] [ 332] [depth= 3] . ( 16 sec) [ -3379.8431] [ 332] [depth= 4] . ( 17 sec) [ -3379.7768] [ 332] [depth= 1] . ( 17 sec) [ -3379.6954] [ 332] [depth= 4] . ( 17 sec) [ -3379.5804] [ 332] [depth= 6] . ( 17 sec) [ -3379.4812] [ 332] [depth= 3] . ( 18 sec) [ -3379.4187] [ 332] [depth= 6] . ( 18 sec) [ -3379.3873] [ 332] [depth= 6] . ( 18 sec) [ -3379.3297] [ 332] [depth= 1] . ( 18 sec) [ -3377.1037] [ 331] [depth= 2] . ( 18 sec) [ -3377.0604] [ 331] [depth= 2] . ( 18 sec) [ -3376.0277] [ 331] [depth= 1] . ( 18 sec) [ -3375.7629] [ 331] [depth= 3] . ( 19 sec) [ -3375.6585] [ 331] [depth= 2] . ( 19 sec) [ -3375.6435] [ 331] [depth= 6] . ( 19 sec) [ -3375.5576] [ 331] [depth= 1] . ( 19 sec) [ -3375.5321] [ 331] [depth= 1] . ( 19 sec) [ -3375.2631] [ 331] [depth= 4] . ( 20 sec) [ -3375.1516] [ 331] [depth= 6] . ( 20 sec) [ -3375.1302] [ 331] [depth= 2] . ( 21 sec) [ -3371.7223] [ 330] [depth= 1] . ( 21 sec) [ -3371.6085] [ 330] [depth= 1] . ( 21 sec) [ -3371.5856] [ 330] [depth= 1] . ( 21 sec) [ -3371.5152] [ 330] [depth= 1] . ( 22 sec) [ -3368.8776] [ 330] [depth= 1] . ( 22 sec) [ -3367.4577] [ 330] [depth= 1] . ( 22 sec) [ -3366.7056] [ 330] [depth= 5] . ( 22 sec) [ -3366.6872] [ 330] [depth= 2] . ( 24 sec) [ -3366.6680] [ 330] [depth= 1] . ( 37 sec) [ -3359.8385] [Branch lengths ] . ( 37 sec) [ -3359.8054] [Ts/ts ratio ][ 2.579618] . ( 39 sec) [ -3359.7922] [ 330] [depth= 4] . ( 41 sec) [ -3359.7815] [ 330] [depth= 3] . ( 41 sec) [ -3359.7509] [ 330] [depth= 2] . ( 42 sec) [ -3359.6674] [ 330] [depth= 1] . ( 74 sec) [ -3359.6448] [ 330] [depth= 8] . ( 94 sec) [ -3359.3880] [Branch lengths ] . ( 94 sec) [ -3359.3877] [Ts/ts ratio ][ 2.572385] . ( 98 sec) [ -3359.3722] [ 330] [depth= 1] . ( 102 sec) [ -3359.3615] [ 330] [depth= 2] . ( 135 sec) [ -3359.3404] [Branch lengths ] . ( 135 sec) [ -3359.3404] [Ts/ts ratio ][ 2.569813] . ( 136 sec) [ -3359.3404] [Topology ] . ( 136 sec) [ -3359.3396] [Topology ] . ( 136 sec) [ -3359.3396] [Ts/ts ratio ][ 2.569813] . Checking for NNIs, optimizing five branches... . ( 141 sec) [ -3359.3395] [Topology ] . Checking for NNIs, optimizing five branches... . ( 146 sec) [ -3359.3393] [Topology ] . Checking for NNIs, optimizing five branches... . ( 150 sec) [ -3359.3392] [Topology ] . Checking for NNIs, optimizing five branches... . ( 155 sec) [ -3359.3379] [Topology ] . Checking for NNIs, optimizing five branches... . ( 160 sec) [ -3359.3345] [Topology ] . Checking for NNIs, optimizing five branches... . ( 165 sec) [ -3359.3344] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3359.334430. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 25 -1.000000 0.000000 0.000000 14 -1.000000 0.000000 0.000000 77 6.163471 0.832000 0.008163 75 5.654472 0.783000 0.021610 46 4.227147 0.838000 0.017159 24 0.582168 0.263000 0.001920 99 30.337249 0.959000 0.007106 58 84.210185 1.000000 0.014929 50 8.598110 0.853000 0.005447 66 3.708503 0.817000 0.010178 64 28.253336 0.955000 0.006688 69 0.450215 0.673000 0.002032 25 -1.000000 0.000000 0.000000 19 -1.000000 0.000000 0.000000 87 19.001880 0.957000 0.004961 8 2.779224 0.711000 0.001156 1 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 35 15.011039 0.915000 0.001531 8 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000002 6 -1.000000 0.000000 0.000002 13 2.297239 0.680000 0.001644 22 7.094598 0.819000 0.002912 39 5.310374 0.780000 0.001420 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 97 43.974248 0.981000 0.009014 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.001444 3 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 32 44.522876 0.976000 0.006219 2 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 85 8.301188 0.873000 0.005840 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 42 15.797054 0.920000 0.001067 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 0.000211 0.000000 0.000000 4 0.006979 0.000000 0.001051 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2716_79x1252_2006.phy_phyml_tree.txt'... . Time used 5h16m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo