.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M3755_77x9918_2008.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 9606 patterns found. (out of a total of 9918 sites) . 1366 sites without polymorphism (13.77%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1774Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=4.000000 LK=-368380.085932 . ( 62 sec) [ -367503.1303] [Alpha ][ 0.583614] . ( 77 sec) [ -367503.1303] [Topology ] . ( 241 sec) [ -364939.8192] [Topology ] . ( 432 sec) [ -363662.9412] [Topology ] . ( 595 sec) [ -363523.9191] [Topology ] . ( 782 sec) [ -363120.4534] [Topology ] . Moving backward . ( 965 sec) [ -362845.5581] [Topology ] . ( 1141 sec) [ -362701.9257] [Topology ] . ( 1308 sec) [ -362655.8062] [Topology ] . Moving backward . ( 1504 sec) [ -362552.5889] [Topology ] . Moving backward . ( 1692 sec) [ -362540.9114] [Topology ] . Moving backward . Before opt ts/t=4.000000 LK=-362540.329723 . ( 1927 sec) [ -362150.2902] [Alpha ][ 0.809992] . ( 1941 sec) [ -362150.2902] [Topology ] . Moving backward . ( 2124 sec) [ -362119.8306] [Topology ] . Moving backward . ( 2312 sec) [ -362109.9363] [Topology ] . Moving backward . ( 2499 sec) [ -362093.7233] [Topology ] . Moving backward . ( 2686 sec) [ -362068.4828] [Topology ] . ( 2853 sec) [ -362041.6952] [Topology ] . ( 3021 sec) [ -362003.0470] [Topology ] . ( 3190 sec) [ -361966.2618] [Topology ] . ( 3359 sec) [ -361956.1475] [Topology ] . ( 3527 sec) [ -361911.1021] [Topology ] . Before opt ts/t=4.000000 LK=-361877.523647 . ( 3751 sec) [ -361876.4117] [Alpha ][ 0.824210] . ( 3764 sec) [ -361876.4117] [Topology ] . ( 3933 sec) [ -361853.9110] [Topology ] . ( 4103 sec) [ -361841.5313] [Topology ] . ( 4270 sec) [ -361836.6303] [Topology ] . ( 4441 sec) [ -361836.2864] [Topology ] . ( 4610 sec) [ -361834.2796] [Topology ] . Moving backward . ( 4799 sec) [ -361831.1059] [Topology ] . ( 4967 sec) [ -361830.7743] [Topology ] . Moving backward . ( 5156 sec) [ -361827.6904] [Topology ] . ( 5326 sec) [ -361826.1886] [Topology ] . Checking for NNIs, optimizing five branches... . ( 8348 sec) [ -361817.8324] [Topology ] . Before opt ts/t=4.000000 LK=-361817.832449 . ( 8420 sec) [ -361817.8168] [Alpha ][ 0.825853] . ( 8440 sec) [ -361817.8168] [Topology ] . ( 8692 sec) [ -361808.3966] [Topology ] . ( 8946 sec) [ -361804.8769] [Topology ] . ( 9201 sec) [ -361802.9725] [Topology ] . ( 9454 sec) [ -361801.4962] [Topology ] . ( 9704 sec) [ -361800.3847] [Topology ] . ( 9957 sec) [ -361799.4679] [Topology ] . (10203 sec) [ -361798.7460] [Topology ] . Checking for NNIs, optimizing five branches... . (12702 sec) [ -361792.0221] [Topology ] . Before opt ts/t=4.000000 LK=-361792.022050 . (12756 sec) [ -361792.0221] [Alpha ][ 0.825853] . (12773 sec) [ -361792.0221] [Topology ] . (12975 sec) [ -361788.3793] [Topology ] . (13173 sec) [ -361781.9505] [Topology ] . (13387 sec) [ -361778.0637] [Topology ] . (13574 sec) [ -361777.0611] [Topology ] . (13777 sec) [ -361776.5719] [Topology ] . (13952 sec) [ -361776.2532] [Topology ] . (14148 sec) [ -361776.0076] [Topology ] . (14324 sec) [ -361775.8165] [Topology ] . Checking for NNIs, optimizing five branches... . (16399 sec) [ -361768.8446] [Topology ] . Before opt ts/t=4.000000 LK=-361768.844591 . (16446 sec) [ -361768.8446] [Alpha ][ 0.825853] . (16460 sec) [ -361768.8446] [Topology ] . (16627 sec) [ -361768.7964] [Topology ] . (16794 sec) [ -361768.7696] [Topology ] . (16961 sec) [ -361768.7479] [Topology ] . (17128 sec) [ -361768.7287] [Topology ] . (17295 sec) [ -361768.7110] [Topology ] . (17462 sec) [ -361768.6945] [Topology ] . Checking for NNIs, optimizing five branches... . (19482 sec) [ -361768.1837] [Topology ] . Before opt ts/t=4.000000 LK=-361768.183740 . (19529 sec) [ -361768.1837] [Alpha ][ 0.825853] . (19543 sec) [ -361768.1837] [Topology ] . (19710 sec) [ -361768.1485] [Topology ] . (19876 sec) [ -361767.7886] [Topology ] . (20044 sec) [ -361767.2749] [Topology ] . (20212 sec) [ -361766.9750] [Topology ] . (20379 sec) [ -361766.6544] [Topology ] . (20546 sec) [ -361765.9549] [Topology ] . (20713 sec) [ -361765.7228] [Topology ] . (20880 sec) [ -361765.5944] [Topology ] . (21047 sec) [ -361765.5164] [Topology ] . Checking for NNIs, optimizing five branches... . (23196 sec) [ -361761.5381] [Topology ] . Before opt ts/t=4.000000 LK=-361761.538135 . (23243 sec) [ -361761.5381] [Alpha ][ 0.825853] . (23257 sec) [ -361761.5381] [Topology ] . (23423 sec) [ -361738.5967] [Topology ] . (23590 sec) [ -361729.0921] [Topology ] . (23756 sec) [ -361725.6550] [Topology ] . Moving backward . (23940 sec) [ -361721.3860] [Topology ] . (24106 sec) [ -361720.0309] [Topology ] . (24271 sec) [ -361719.7704] [Topology ] . (24436 sec) [ -361719.6702] [Topology ] . (24602 sec) [ -361719.6249] [Topology ] . (24768 sec) [ -361719.6018] [Topology ] . Checking for NNIs, optimizing five branches... . (26940 sec) [ -361719.5034] [Topology ] . Before opt ts/t=4.000000 LK=-361719.503352 . (26987 sec) [ -361719.5034] [Alpha ][ 0.825853] . (27000 sec) [ -361719.5034] [Topology ] . (27167 sec) [ -361719.4959] [Topology ] . (27335 sec) [ -361719.4916] [Topology ] . (27502 sec) [ -361719.4890] [Topology ] . (27669 sec) [ -361719.4874] [Topology ] . (27836 sec) [ -361719.4865] [Topology ] . Checking for NNIs, optimizing five branches... . (29799 sec) [ -361714.7227] [Topology ] . Before opt ts/t=4.000000 LK=-361714.722712 . (29846 sec) [ -361714.7227] [Alpha ][ 0.825853] . (29860 sec) [ -361714.7227] [Topology ] . (30025 sec) [ -361714.6926] [Topology ] . (30191 sec) [ -361714.6873] [Topology ] . (30356 sec) [ -361714.6856] [Topology ] . (30522 sec) [ -361714.6848] [Topology ] . Checking for NNIs, optimizing five branches... . (32563 sec) [ -361714.5545] [Topology ] . Before opt ts/t=4.000000 LK=-361714.554504 . (32611 sec) [ -361714.5545] [Alpha ][ 0.825853] . (32624 sec) [ -361714.5545] [Topology ] . (32790 sec) [ -361714.5534] [Topology ] . (32956 sec) [ -361714.5529] [Topology ] . Checking for NNIs, optimizing five branches... . (35059 sec) [ -361708.1427] [Topology ] . Before opt ts/t=4.000000 LK=-361708.142745 . (35106 sec) [ -361708.1427] [Alpha ][ 0.825853] . (35120 sec) [ -361708.1427] [Topology ] . (35287 sec) [ -361708.1287] [Topology ] . (35454 sec) [ -361708.1265] [Topology ] . (35622 sec) [ -361708.1258] [Topology ] . Checking for NNIs, optimizing five branches... . (37701 sec) [ -361707.7607] [Topology ] . Before opt ts/t=4.000000 LK=-361707.760740 . (37748 sec) [ -361707.7600] [Alpha ][ 0.826679] . (37761 sec) [ -361707.7600] [Topology ] . (37928 sec) [ -361707.7504] [Topology ] . (38096 sec) [ -361707.7488] [Topology ] . (38263 sec) [ -361707.7482] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=4.000000 LK=-361707.748238 . (40389 sec) [ -361707.7482] [Alpha ][ 0.826679] . (40402 sec) [ -361707.7482] [Topology ] . (40569 sec) [ -361707.7479] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -361707.747854. . Printing the most likely tree in file 'proteic_M3755_77x9918_2008.phy_phyml_tree.txt'... . Time used 12h25m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo