.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2512_14x717_2006.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... . 703 patterns found. (out of a total of 717 sites) . 39 sites without polymorphism (5.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21213.2541] [ 4565] [depth= 1] . ( 2 sec) [ -21191.4385] [ 4560] [depth= 1] . ( 3 sec) [ -21179.2222] [ 4560] [depth= 1] . ( 3 sec) [ -21173.4949] [ 4560] [depth= 1] . ( 5 sec) [ -21107.6008] [ 4569] [depth= 1] . ( 5 sec) [ -21065.6352] [ 4613] [depth= 2] . ( 6 sec) [ -20983.3782] [ 4552] [depth= 2] . ( 6 sec) [ -20619.0294] [ 4548] [depth= 1] . ( 7 sec) [ -20520.6622] [ 4543] [depth= 1] . ( 7 sec) [ -20445.7479] [ 4544] [depth= 1] . ( 8 sec) [ -20436.1947] [ 4538] [depth= 2] . ( 8 sec) [ -20429.4013] [ 4529] [depth= 1] . ( 8 sec) [ -20420.9126] [ 4540] [depth= 1] . ( 9 sec) [ -20411.6535] [ 4552] [depth= 1] . ( 9 sec) [ -20403.5470] [ 4544] [depth= 1] . ( 9 sec) [ -20375.2390] [ 4534] [depth= 1] . ( 11 sec) [ -20363.5590] [ 4542] [depth= 1] . ( 12 sec) [ -20189.4390] [Branch lengths ] . ( 15 sec) [ -20188.6810] [ 4534] [depth= 1] . ( 16 sec) [ -20185.9393] [ 4523] [depth= 1] . ( 18 sec) [ -20182.2139] [ 4525] [depth= 1] . ( 18 sec) [ -20180.8272] [ 4512] [depth= 2] . ( 22 sec) [ -20179.9699] [ 4517] [depth= 1] . ( 24 sec) [ -20151.6931] [Branch lengths ] . ( 32 sec) [ -20146.4927] [ 4512] [depth= 1] . ( 34 sec) [ -20133.7507] [Branch lengths ] . ( 44 sec) [ -20129.5442] [Branch lengths ] . ( 44 sec) [ -20129.5442] [Topology ] . ( 46 sec) [ -20128.6514] [Topology ] . ( 48 sec) [ -20128.2515] [Topology ] . ( 50 sec) [ -20127.9889] [Topology ] . ( 52 sec) [ -20127.8028] [Topology ] . ( 54 sec) [ -20127.6667] [Topology ] . ( 57 sec) [ -20127.5653] [Topology ] . ( 57 sec) [ -20127.5653] [Topology ] . ( 59 sec) [ -20127.4888] [Topology ] . ( 61 sec) [ -20127.4303] [Topology ] . ( 63 sec) [ -20127.3850] [Topology ] . ( 65 sec) [ -20127.3496] [Topology ] . ( 67 sec) [ -20127.3216] [Topology ] . ( 70 sec) [ -20127.2991] [Topology ] . ( 70 sec) [ -20127.2991] [Topology ] . ( 72 sec) [ -20127.2810] [Topology ] . ( 74 sec) [ -20127.2663] [Topology ] . ( 76 sec) [ -20127.2541] [Topology ] . ( 78 sec) [ -20127.2441] [Topology ] . ( 80 sec) [ -20127.2357] [Topology ] . ( 82 sec) [ -20127.2165] [Topology ] . ( 84 sec) [ -20126.8208] [Topology ] . ( 86 sec) [ -20126.7769] [Topology ] . ( 88 sec) [ -20126.7622] [Topology ] . ( 90 sec) [ -20126.7548] [Topology ] . ( 92 sec) [ -20126.7501] [Topology ] . ( 94 sec) [ -20126.7466] [Topology ] . ( 96 sec) [ -20126.7438] [Topology ] . ( 98 sec) [ -20126.7415] [Topology ] . ( 100 sec) [ -20126.7395] [Topology ] . ( 102 sec) [ -20126.7379] [Topology ] . ( 102 sec) [ -20126.7379] [Topology ] . ( 104 sec) [ -20126.7365] [Topology ] . ( 106 sec) [ -20126.7352] [Topology ] . ( 108 sec) [ -20126.7341] [Topology ] . ( 110 sec) [ -20126.7332] [Topology ] . ( 110 sec) [ -20126.7332] [Topology ] . ( 112 sec) [ -20126.7324] [Topology ] . Checking for NNIs, optimizing five branches... . ( 144 sec) [ -20125.2215] [Topology ] . Checking for NNIs, optimizing five branches... . ( 174 sec) [ -20125.2167] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20125.216693. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 95 44.047538 0.998000 2.210386 57 6.608715 0.787000 0.734747 61 7.893870 0.895000 6.213759 89 59.706002 0.996000 19.828924 46 25.310002 0.965000 14.664163 7 -1.000000 0.000000 0.000344 60 1.595778 0.701000 0.635276 86 42.654454 0.997000 1.990152 40 4.771459 0.810000 0.271522 31 0.951502 0.196000 0.159784 47 12.405868 0.861000 0.296318 . Printing the most likely tree in file 'proteic_M2512_14x717_2006.phy_phyml_tree.txt'... . Time used 4h39m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo