.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data19.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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 . Compressing sequences... . 423 patterns found. (out of a total of 500 sites) . 70 sites without polymorphism (14.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9166.391103 . ( 1 sec) [ -9163.6827] [GTR parameters ] . ( 1 sec) [ -9163.5645] [Alpha ][ 0.962775] . ( 1 sec) [ -9163.5645] [Topology ] . ( 2 sec) [ -9118.6274] [Topology ] . ( 3 sec) [ -9110.9425] [Topology ] . ( 4 sec) [ -9108.0749] [Topology ] . ( 5 sec) [ -9106.8802] [Topology ] . ( 6 sec) [ -9106.2436] [Topology ] . ( 6 sec) [ -9105.8925] [Topology ] . ( 7 sec) [ -9105.7386] [Topology ] . ( 8 sec) [ -9105.6590] [Topology ] . ( 9 sec) [ -9105.6166] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9105.593658 . ( 17 sec) [ -9105.5414] [GTR parameters ] . ( 17 sec) [ -9105.4855] [Alpha ][ 0.986389] . ( 17 sec) [ -9105.4855] [Topology ] . ( 17 sec) [ -9105.4674] [Topology ] . ( 18 sec) [ -9105.4587] [Topology ] . ( 19 sec) [ -9105.4542] [Topology ] . ( 20 sec) [ -9105.4518] [Topology ] . ( 21 sec) [ -9105.4505] [Topology ] . ( 22 sec) [ -9105.4498] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -9105.4495] [Topology ] . Before opt ts/t=1.000000 LK=-9105.449465 . ( 31 sec) [ -9105.4494] [GTR parameters ] . ( 31 sec) [ -9105.4489] [Alpha ][ 0.988775] . ( 31 sec) [ -9105.4489] [Topology ] . ( 32 sec) [ -9105.4484] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9105.448438 . ( 39 sec) [ -9105.4484] [GTR parameters ] . ( 39 sec) [ -9105.4484] [Alpha ][ 0.988775] . ( 39 sec) [ -9105.4484] [Topology ] . ( 40 sec) [ -9105.4482] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -9163.6827] [GTR parameters ] . ( 53 sec) [ -9163.5645] [Alpha ][ 0.962775] . ( 54 sec) [ -9162.0615] [ 1979] [depth= 1] . ( 54 sec) [ -9161.7501] [ 1981] [depth= 1] . ( 55 sec) [ -9159.0573] [ 1980] [depth= 1] . ( 55 sec) [ -9159.0379] [ 1985] [depth= 1] . ( 56 sec) [ -9158.6642] [ 1989] [depth= 1] . ( 56 sec) [ -9157.5898] [ 1984] [depth= 1] . ( 56 sec) [ -9153.8178] [ 1989] [depth= 1] . ( 56 sec) [ -9149.8869] [ 1993] [depth= 1] . ( 56 sec) [ -9149.7471] [ 1992] [depth= 1] . ( 57 sec) [ -9146.2539] [ 1993] [depth= 1] . ( 57 sec) [ -9144.0859] [ 1995] [depth= 1] . ( 57 sec) [ -9138.4448] [ 1991] [depth= 1] . ( 57 sec) [ -9134.7219] [ 1995] [depth= 1] . ( 58 sec) [ -9134.0681] [ 1996] [depth= 1] . ( 58 sec) [ -9133.6594] [ 1994] [depth= 1] . ( 58 sec) [ -9133.1926] [ 1996] [depth= 1] . ( 58 sec) [ -9132.5205] [ 1995] [depth= 1] . ( 58 sec) [ -9110.6705] [Branch lengths ] . ( 59 sec) [ -9110.6132] [GTR parameters ] . ( 59 sec) [ -9110.5887] [Alpha ][ 0.979168] . ( 60 sec) [ -9109.7161] [ 1993] [depth= 1] . ( 60 sec) [ -9109.4972] [ 1988] [depth= 1] . ( 63 sec) [ -9105.8178] [Branch lengths ] . ( 63 sec) [ -9105.8110] [GTR parameters ] . ( 63 sec) [ -9105.8083] [Alpha ][ 0.984572] . ( 68 sec) [ -9105.5127] [Branch lengths ] . ( 92 sec) [ -9105.4612] [Branch lengths ] . ( 92 sec) [ -9105.4612] [Topology ] . ( 93 sec) [ -9105.4552] [Topology ] . ( 94 sec) [ -9105.4529] [Topology ] . ( 95 sec) [ -9105.4517] [Topology ] . ( 96 sec) [ -9105.4511] [Topology ] . ( 96 sec) [ -9105.4508] [GTR parameters ] . ( 97 sec) [ -9105.4492] [Alpha ][ 0.988743] . ( 97 sec) [ -9105.4492] [Topology ] . ( 98 sec) [ -9105.4487] [Topology ] . ( 98 sec) [ -9105.4487] [GTR parameters ] . ( 98 sec) [ -9105.4487] [Alpha ][ 0.988743] . Checking for NNIs, optimizing five branches... . ( 105 sec) [ -9105.4484] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9105.448221 . Log likelihood obtained after SPR moves : -9105.448397 . Log likelihood of the current tree: -9105.448221. . Printing the most likely tree in file 'data19.phy_phyml_tree.txt'... . Time used 0h1m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo