.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1993_28x93_2004.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : LG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : no . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 79 patterns found. (out of a total of 93 sites) . 26 sites without polymorphism (27.96%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -2034.0343] [ 343] [depth= 1] . ( 1 sec) [ -2031.7032] [ 344] [depth= 1] . ( 6 sec) [ -2025.4531] [ 342] [depth= 1] . ( 6 sec) [ -2024.4068] [ 341] [depth= 1] . ( 6 sec) [ -2022.0912] [ 340] [depth= 2] . ( 6 sec) [ -2017.5537] [ 340] [depth= 1] . ( 9 sec) [ -2016.3068] [ 340] [depth= 2] . ( 11 sec) [ -2015.8834] [ 342] [depth= 1] . ( 12 sec) [ -2014.6518] [ 343] [depth= 3] . ( 12 sec) [ -2013.3501] [ 343] [depth= 1] . ( 13 sec) [ -2013.1036] [ 342] [depth= 1] . ( 21 sec) [ -2011.1386] [ 343] [depth= 1] . ( 21 sec) [ -2007.3671] [ 343] [depth= 2] . ( 21 sec) [ -2005.9142] [ 343] [depth= 1] . ( 21 sec) [ -2005.8196] [ 343] [depth= 1] . ( 21 sec) [ -2005.7888] [ 343] [depth= 1] . ( 23 sec) [ -1999.8205] [Branch lengths ] . ( 35 sec) [ -1999.3181] [ 342] [depth= 1] . ( 40 sec) [ -1999.2976] [ 343] [depth= 1] . ( 48 sec) [ -1999.0533] [ 342] [depth= 1] . ( 52 sec) [ -1998.2082] [Branch lengths ] . ( 69 sec) [ -1998.1940] [ 343] [depth= 3] . ( 73 sec) [ -1997.9621] [ 342] [depth= 1] . ( 81 sec) [ -1997.8770] [Branch lengths ] . ( 81 sec) [ -1997.8770] [Topology ] . ( 82 sec) [ -1997.8619] [Topology ] . ( 83 sec) [ -1997.8572] [Topology ] . ( 83 sec) [ -1997.8550] [Topology ] . ( 84 sec) [ -1997.8537] [Topology ] . ( 84 sec) [ -1997.8531] [Topology ] . ( 85 sec) [ -1997.8531] [Topology ] . ( 85 sec) [ -1997.8527] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1997.852660. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 85 6.548755 0.856000 0.194963 100 59.443951 0.997000 0.392602 23 3.749851 0.724000 0.059749 20 0.733240 0.183000 0.060486 25 1.940533 0.719000 0.031334 86 33.299653 0.979000 0.135876 78 33.375524 0.975000 0.131116 27 3.962198 0.472000 0.038373 57 34.529175 0.965000 0.117464 18 0.599309 0.465000 0.011734 21 1.034116 0.399000 0.030339 35 2.967709 0.744000 0.019282 57 8.417490 0.840000 0.031656 100 31.517592 0.973000 0.085781 77 15.482499 0.900000 0.063254 96 13.507945 0.934000 0.061188 35 3.198718 0.733000 0.019085 53 10.926704 0.888000 0.070944 49 14.391348 0.884000 0.039809 31 1.334201 0.717000 0.007947 41 13.241434 0.914000 0.020659 84 34.096809 0.981000 0.067427 14 -1.000000 0.000000 0.000001 39 0.126095 0.000000 0.079663 67 0.902437 0.162000 0.065209 . Printing the most likely tree in file 'proteic_M1993_28x93_2004.phy_phyml_tree.txt'... . Time used 2h17m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo