. 2282 patterns found (out of a total of 3618 sites). . 1338 sites without polymorphism (36.98%). . Computing pairwise distances... . Building BioNJ tree... oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM10 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Initial values of parameters . Sequence filename: input.phy . Sequence format : interleaved . Data type : aa - The number of states: 64 . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of amino acids substitution: /usr/local/phylogeny/phyml/dat/Wmatrix-11_mtREV JTT-ML91+mod-0 . Number of taxa: 69 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 1.449950 * aa_fitness(a,b) + -1.500000 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.016440 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000000 transition/transversion m_tc|ag / m_[tc][ag] 1.000000 T <-> C / transition m_tc / m_tc|ag 1.000000 A <-> G / transition m_ag / m_tc|ag 1.000000 T <-> C / transversion m_tc / m_[tc][ag] 1.000000 A <-> G / transversion m_ag / m_[tc][ag] 1.000000 T <-> A / transversion m_ta / m_[tc][ag] 1.000000 T <-> G / transversion m_tg / m_[tc][ag] 1.000000 C <-> A / transversion m_ca / m_[tc][ag] 1.000000 C <-> G / transversion m_cg / m_[tc][ag] 1.000000 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.250000 0.250000 0.250000 0.250000 - f(A) = 0.250000 - f(C) = 0.250000 - f(G) = 0.250000 - f(T) = 0.250000 . Nucleotides frequencies for codon usage: ACGT : 0.250000 0.250000 0.250000 0.250000 . Codon frequencies: from_sequence? 1 : TTT F 0.030325 TCT S 0.012559 TAT Y 0.017253 TGT C 0.003041 TTC F 0.030325 TCC S 0.012559 TAC Y 0.017253 TGC C 0.003041 TTA L 0.027281 TCA S 0.012559 TAA * 0.000000 TGA W 0.013752 TTG L 0.027281 TCG S 0.012559 TAG * 0.000000 TGG W 0.013752 CTT L 0.027281 CCT P 0.013443 CAT H 0.013756 CGT R 0.004408 CTC L 0.027281 CCC P 0.013443 CAC H 0.013756 CGC R 0.004408 CTA L 0.027281 CCA P 0.013443 CAA Q 0.011949 CGA R 0.004408 CTG L 0.027281 CCG P 0.013443 CAG Q 0.011949 CGG R 0.004408 ATT I 0.045323 ACT T 0.021581 AAT N 0.021292 AGT S 0.012559 ATC I 0.045323 ACC T 0.021581 AAC N 0.021292 AGC S 0.012559 ATA M 0.030730 ACA T 0.021581 AAA K 0.012582 AGA * 0.000000 ATG M 0.030730 ACG T 0.021581 AAG K 0.012582 AGG * 0.000000 GTT V 0.010715 GCT A 0.016606 GAT D 0.008900 GGT G 0.013174 GTC V 0.010715 GCC A 0.016606 GAC D 0.008900 GGC G 0.013174 GTA V 0.010715 GCA A 0.016606 GAA E 0.011722 GGA G 0.013174 GTG V 0.010715 GCG A 0.016606 GAG E 0.011722 GGG G 0.013174 . WARNING: this analysis requires at least 404 MB of memory space. . ( 20 sec) [ -145889.8290] [Branch lengths ] . ( 52 sec) [ -145293.8433] [Selective constraints on amino acids ][1.546420 * aa_fitness(a,b) + -1.683269 * (1-delta(a,b))] . ( 103 sec) [ -144252.7124] [GTR parameters ][rr_val: 0.000000 1.670056 0.881396 1.000000 1.000000 1.000000] . ( 125 sec) [ -142555.4709] [Branch lengths ] . ( 157 sec) [ -142207.1035] [Selective constraints on amino acids ][1.457170 * aa_fitness(a,b) + -1.806464 * (1-delta(a,b))] . ( 212 sec) [ -142121.8458] [GTR parameters ][rr_val: 0.000000 1.931809 0.856051 1.000000 1.000000 1.000000] . ( 234 sec) [ -142077.8019] [Branch lengths ] . ( 266 sec) [ -141842.6615] [Selective constraints on amino acids ][1.377423 * aa_fitness(a,b) + -1.896441 * (1-delta(a,b))] . ( 302 sec) [ -141837.0525] [GTR parameters ][rr_val: 0.000000 2.007847 0.867079 1.000000 1.000000 1.000000] . ( 324 sec) [ -141836.4127] [Branch lengths ] . ( 358 sec) [ -141682.6294] [Selective constraints on amino acids ][1.312210 * aa_fitness(a,b) + -1.966617 * (1-delta(a,b))] . ( 392 sec) [ -141680.4826] [GTR parameters ][rr_val: 0.000000 2.022045 0.886498 1.000000 1.000000 1.000000] . ( 414 sec) [ -141679.0149] [Branch lengths ] . ( 446 sec) [ -141576.1091] [Selective constraints on amino acids ][1.258627 * aa_fitness(a,b) + -2.022687 * (1-delta(a,b))] . ( 483 sec) [ -141574.0451] [GTR parameters ][rr_val: 0.000000 2.019313 0.905313 1.000000 1.000000 1.000000] . ( 505 sec) [ -141571.9628] [Branch lengths ] . ( 538 sec) [ -141502.4639] [Selective constraints on amino acids ][1.214242 * aa_fitness(a,b) + -2.067916 * (1-delta(a,b))] . ( 574 sec) [ -141500.8513] [GTR parameters ][rr_val: 0.000000 2.014175 0.921683 1.000000 1.000000 1.000000] . ( 596 sec) [ -141498.8542] [Branch lengths ] . ( 629 sec) [ -141452.0364] [Selective constraints on amino acids ][1.177378 * aa_fitness(a,b) + -2.104193 * (1-delta(a,b))] . ( 665 sec) [ -141450.9081] [GTR parameters ][rr_val: 0.000000 2.010262 0.935362 1.000000 1.000000 1.000000] . ( 687 sec) [ -141449.1294] [Branch lengths ] . ( 718 sec) [ -141418.7888] [Selective constraints on amino acids ][1.147884 * aa_fitness(a,b) + -2.131359 * (1-delta(a,b))] . ( 760 sec) [ -141418.0692] [GTR parameters ][rr_val: 0.000000 2.008047 0.946310 1.000000 1.000000 1.000000] . ( 783 sec) [ -141416.4752] [Branch lengths ] . ( 815 sec) [ -141396.0799] [Selective constraints on amino acids ][1.123307 * aa_fitness(a,b) + -2.152374 * (1-delta(a,b))] . ( 844 sec) [ -141395.5899] [GTR parameters ][rr_val: 0.000000 2.007149 0.956472 1.000000 1.000000 1.000000] . ( 866 sec) [ -141394.0657] [Branch lengths ] . ( 899 sec) [ -141380.2988] [Selective constraints on amino acids ][1.102707 * aa_fitness(a,b) + -2.168292 * (1-delta(a,b))] . ( 941 sec) [ -141380.0381] [GTR parameters ][rr_val: 0.000000 2.007092 0.963431 1.000000 1.000000 1.000000] . ( 963 sec) [ -141378.6527] [Branch lengths ] . ( 994 sec) [ -141369.5624] [Selective constraints on amino acids ][1.085556 * aa_fitness(a,b) + -2.179752 * (1-delta(a,b))] . ( 1036 sec) [ -141369.3544] [GTR parameters ][rr_val: 0.000000 2.008252 0.969652 1.000000 1.000000 1.000000] . ( 1057 sec) [ -141368.0169] [Branch lengths ] . ( 1092 sec) [ -141361.9984] [Selective constraints on amino acids ][1.071212 * aa_fitness(a,b) + -2.187493 * (1-delta(a,b))] . ( 1133 sec) [ -141361.8517] [GTR parameters ][rr_val: 0.000000 2.009228 0.974789 1.000000 1.000000 1.000000] . ( 1156 sec) [ -141360.5198] [Branch lengths ] . ( 1190 sec) [ -141356.5351] [Selective constraints on amino acids ][1.059197 * aa_fitness(a,b) + -2.192079 * (1-delta(a,b))] . ( 1230 sec) [ -141356.4277] [GTR parameters ][rr_val: 0.000000 2.010478 0.979120 1.000000 1.000000 1.000000] . ( 1253 sec) [ -141355.1019] [Branch lengths ] . ( 1288 sec) [ -141352.4548] [Selective constraints on amino acids ][1.049120 * aa_fitness(a,b) + -2.196350 * (1-delta(a,b))] . ( 1329 sec) [ -141352.3372] [GTR parameters ][rr_val: 0.000000 2.007666 0.983245 1.000000 1.000000 1.000000] . ( 1351 sec) [ -141351.3798] [Branch lengths ] . ( 1382 sec) [ -141349.5861] [Selective constraints on amino acids ][1.040723 * aa_fitness(a,b) + -2.196350 * (1-delta(a,b))] . ( 1416 sec) [ -141349.5351] [GTR parameters ][rr_val: 0.000000 2.010686 0.985726 1.000000 1.000000 1.000000]