.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1989_18x173_2004.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 7 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 139 patterns found. (out of a total of 173 sites) . 46 sites without polymorphism (26.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3205.9405] [Alpha ][ 0.715572] . ( 0 sec) [ -3205.9405] [Topology ] . ( 0 sec) [ -3185.8438] [Topology ] . ( 1 sec) [ -3182.6057] [Topology ] . ( 2 sec) [ -3180.8613] [Topology ] . ( 2 sec) [ -3180.4036] [Topology ] . ( 3 sec) [ -3180.3247] [Topology ] . ( 3 sec) [ -3180.2902] [Topology ] . ( 4 sec) [ -3180.2719] [Topology ] . ( 5 sec) [ -3180.2615] [Topology ] . ( 5 sec) [ -3180.2554] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -3179.9529] [Alpha ][ 0.791776] . ( 9 sec) [ -3179.9529] [Topology ] . ( 10 sec) [ -3179.9261] [Topology ] . ( 10 sec) [ -3179.9145] [Topology ] . ( 11 sec) [ -3179.9081] [Topology ] . ( 12 sec) [ -3179.9046] [Topology ] . ( 12 sec) [ -3179.9026] [Topology ] . ( 13 sec) [ -3179.9014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -3179.8991] [Alpha ][ 0.798974] . ( 17 sec) [ -3179.8991] [Topology ] . ( 17 sec) [ -3179.8981] [Topology ] . ( 18 sec) [ -3179.8975] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -3179.8975] [Alpha ][ 0.799773] . ( 22 sec) [ -3179.8975] [Topology ] . ( 23 sec) [ -3179.8971] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 31 sec) [ -3205.9405] [Alpha ][ 0.715572] . ( 32 sec) [ -3204.8230] [ 588] [depth= 1] . ( 32 sec) [ -3204.4975] [ 588] [depth= 1] . ( 32 sec) [ -3202.1815] [ 588] [depth= 1] . ( 32 sec) [ -3201.6828] [ 588] [depth= 1] . ( 32 sec) [ -3201.4585] [ 588] [depth= 1] . ( 33 sec) [ -3201.3209] [ 588] [depth= 1] . ( 33 sec) [ -3200.3034] [ 590] [depth= 1] . ( 34 sec) [ -3196.8229] [ 588] [depth= 1] . ( 34 sec) [ -3194.9065] [ 588] [depth= 1] . ( 36 sec) [ -3194.8109] [ 590] [depth= 1] . ( 36 sec) [ -3194.0856] [ 588] [depth= 1] . ( 36 sec) [ -3192.5816] [ 587] [depth= 1] . ( 37 sec) [ -3188.0278] [ 586] [depth= 2] . ( 38 sec) [ -3187.7771] [ 587] [depth= 1] . ( 39 sec) [ -3181.9854] [Branch lengths ] . ( 39 sec) [ -3181.8290] [Alpha ][ 0.769967] . ( 42 sec) [ -3181.0234] [ 587] [depth= 1] . ( 49 sec) [ -3180.0617] [Branch lengths ] . ( 49 sec) [ -3180.0407] [Alpha ][ 0.790686] . ( 59 sec) [ -3179.9257] [Branch lengths ] . ( 59 sec) [ -3179.9257] [Topology ] . ( 60 sec) [ -3179.9121] [Topology ] . ( 60 sec) [ -3179.9069] [Topology ] . ( 61 sec) [ -3179.9042] [Topology ] . ( 61 sec) [ -3179.9027] [Topology ] . ( 62 sec) [ -3179.9018] [Topology ] . ( 62 sec) [ -3179.8986] [Alpha ][ 0.799119] . ( 62 sec) [ -3179.8986] [Topology ] . ( 62 sec) [ -3179.8978] [Topology ] . ( 63 sec) [ -3179.8978] [Alpha ][ 0.799119] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3179.897122 . Log likelihood obtained after SPR moves : -3179.897758 . Log likelihood of the current tree: -3179.897122. . Printing the most likely tree in file 'proteic_M1989_18x173_2004.phy_phyml_tree.txt'... . Time used 0h1m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 66.73user 0.00system 1:07.16elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps