.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1372_23x394_2003.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 . 3 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 246 patterns found. (out of a total of 394 sites) . 162 sites without polymorphism (41.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4458.6632] [ 649] [depth= 2] . ( 2 sec) [ -4457.5175] [ 652] [depth= 1] . ( 4 sec) [ -4455.4422] [ 649] [depth= 1] . ( 4 sec) [ -4449.1751] [ 647] [depth= 2] . ( 4 sec) [ -4445.2605] [ 644] [depth= 1] . ( 5 sec) [ -4444.6606] [ 645] [depth= 6] . ( 5 sec) [ -4441.6806] [ 645] [depth= 5] . ( 7 sec) [ -4440.9291] [ 644] [depth= 1] . ( 7 sec) [ -4440.7554] [ 645] [depth= 1] . ( 9 sec) [ -4439.2212] [ 645] [depth= 1] . ( 9 sec) [ -4437.6101] [ 644] [depth= 1] . ( 12 sec) [ -4436.7060] [ 644] [depth= 1] . ( 16 sec) [ -4432.4144] [ 645] [depth= 2] . ( 24 sec) [ -4432.0619] [ 645] [depth= 1] . ( 26 sec) [ -4431.8483] [ 645] [depth= 1] . ( 29 sec) [ -4431.6504] [ 645] [depth= 1] . ( 30 sec) [ -4419.3716] [Branch lengths ] . ( 31 sec) [ -4416.4755] [ 647] [depth= 2] . ( 36 sec) [ -4416.2902] [ 648] [depth= 7] . ( 39 sec) [ -4415.2969] [ 648] [depth= 6] . ( 44 sec) [ -4414.0861] [ 648] [depth= 1] . ( 50 sec) [ -4413.6853] [ 648] [depth= 1] . ( 77 sec) [ -4411.6265] [Branch lengths ] . ( 134 sec) [ -4411.5393] [Branch lengths ] . ( 134 sec) [ -4411.5393] [Topology ] . ( 136 sec) [ -4411.5347] [Topology ] . ( 137 sec) [ -4411.5331] [Topology ] . ( 139 sec) [ -4411.5324] [Topology ] . ( 139 sec) [ -4411.5324] [Topology ] . ( 140 sec) [ -4411.5320] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4411.532020. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 55.710237 0.998000 0.159680 93 8.854398 0.892000 0.058865 98 66.608113 0.997000 0.110357 43 4.694628 0.644000 0.020525 71 14.748402 0.935000 0.056009 73 23.383470 0.951000 0.049462 5 1.360719 0.678000 0.002681 7 3.833149 0.742000 0.002685 7 9.332636 0.873000 0.007550 20 25.985568 0.935000 0.010559 13 3.007398 0.745000 0.006156 14 2.685256 0.481000 0.004954 100 91.892247 0.999000 0.046257 89 25.333328 0.959000 0.026555 4 0.887004 0.204000 0.002476 7 4.571374 0.777000 0.003210 14 7.162458 0.778000 0.002587 21 7.767283 0.794000 0.002574 93 123.311253 1.000000 0.037013 36 1.276401 0.264000 0.004999 . Printing the most likely tree in file 'proteic_M1372_23x394_2003.phy_phyml_tree.txt'... . Time used 3h25m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo