. 80 patterns found (out of a total of 81 sites). . 0 sites without polymorphism (0.00%). . Computing pairwise distances... . Building BioNJ tree... oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Initial values of parameters . Sequence filename: 20110203_155022.txt . Data type : codon . Sequence format : interleaved . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of codons substitution: /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11 . Number of taxa: 4 . Discrete Selection: No . Selective constraints on amino acids: optimize? 0 1 : 0.385234 * aa_fitness[i,j] + -0.000000 . Scale parameter of Gamma distribution: optimize? 0 : 0.917608 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.307849 2.215535 1.010220 1.065729 1.085499 0.890831 transversion m_[tc][ag] 0.307849 transition/transversion m_tc|ag / m_[tc][ag] 2.215535 T <-> C / transition m_tc / m_tc|ag 0.989780 A <-> G / transition m_ag / m_tc|ag 1.010220 T <-> C / transversion m_tc / m_[tc][ag] 2.192892 A <-> G / transversion m_ag / m_[tc][ag] 2.238178 T <-> A / transversion m_ta / m_[tc][ag] 1.065729 T <-> G / transversion m_tg / m_[tc][ag] 1.085499 C <-> A / transversion m_ca / m_[tc][ag] 0.890831 C <-> G / transversion m_cg / m_[tc][ag] 0.957941 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.268305 0.195920 0.239202 0.296573 - f(A) = 0.268305 - f(C) = 0.195920 - f(G) = 0.239202 - f(T) = 0.296573 . Codon frequencies: from_sequence? 1 : TTT F 0.017102 TTC F 0.020188 TTA L 0.010929 TTG L 0.010929 TCT S 0.014015 TCC S 0.010929 TCA S 0.017102 TCG S 0.010929 TAT Y 0.023275 TAC Y 0.017102 TAA * 0.000000 TAG * 0.000000 TGT C 0.001670 TGC C 0.001670 TGA * 0.000000 TGG W 0.023275 CTT L 0.007843 CTC L 0.004756 CTA L 0.014015 CTG L 0.004756 CCT P 0.020188 CCC P 0.010929 CCA P 0.007843 CCG P 0.007843 CAT H 0.004756 CAC H 0.001670 CAA Q 0.014015 CAG Q 0.014015 CGT R 0.010929 CGC R 0.014015 CGA R 0.014015 CGG R 0.010929 ATT I 0.007843 ATC I 0.010929 ATA I 0.007843 ATG M 0.029447 ACT T 0.004756 ACC T 0.007843 ACA T 0.001670 ACG T 0.001670 AAT N 0.041793 AAC N 0.007843 AAA K 0.060312 AAG K 0.075744 AGT S 0.020188 AGC S 0.010929 AGA R 0.010929 AGG R 0.004756 GTT V 0.007843 GTC V 0.007843 GTA V 0.007843 GTG V 0.014015 GCT A 0.032534 GCC A 0.026361 GCA A 0.026361 GCG A 0.032534 GAT D 0.017102 GAC D 0.026361 GAA E 0.051052 GAG E 0.057225 GGT G 0.014015 GGC G 0.010929 GGA G 0.007843 GGG G 0.014015 . ( 0 sec) [ -1010.3420] [Branch lengths ] . ( 0 sec) [ -1008.1041] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -0.571119] . ( 0 sec) [ -1006.1551] [Branch lengths ] . ( 0 sec) [ -1005.9634] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -0.714021] . ( 0 sec) [ -1005.5257] [Branch lengths ] . ( 0 sec) [ -1005.1529] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -0.901763] . ( 1 sec) [ -1004.8864] [Branch lengths ] . ( 1 sec) [ -1004.6427] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.044825] . ( 1 sec) [ -1004.4550] [Branch lengths ] . ( 1 sec) [ -1004.2143] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.180533] . ( 1 sec) [ -1004.0512] [Branch lengths ] . ( 1 sec) [ -1003.8782] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.290855] . ( 1 sec) [ -1003.7474] [Branch lengths ] . ( 1 sec) [ -1003.5766] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.396693] . ( 1 sec) [ -1003.4569] [Branch lengths ] . ( 1 sec) [ -1003.3248] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.488229] . ( 1 sec) [ -1003.2214] [Branch lengths ] . ( 2 sec) [ -1003.0817] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.579968] . ( 2 sec) [ -1002.9832] [Branch lengths ] . ( 2 sec) [ -1002.8758] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.658522] . ( 2 sec) [ -1002.7912] [Branch lengths ] . ( 2 sec) [ -1002.6747] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.738662] . ( 2 sec) [ -1002.5917] [Branch lengths ] . ( 2 sec) [ -1002.5002] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.808342] . ( 2 sec) [ -1002.4272] [Branch lengths ] . ( 2 sec) [ -1002.3270] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.880020] . ( 2 sec) [ -1002.2542] [Branch lengths ] . ( 2 sec) [ -1002.1731] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -1.943529] . ( 2 sec) [ -1002.1077] [Branch lengths ] . ( 3 sec) [ -1002.0176] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.009494] . ( 3 sec) [ -1001.9518] [Branch lengths ] . ( 3 sec) [ -1001.8775] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.068554] . ( 3 sec) [ -1001.8176] [Branch lengths ] . ( 3 sec) [ -1001.7343] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.130354] . ( 3 sec) [ -1001.6731] [Branch lengths ] . ( 3 sec) [ -1001.6040] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.185947] . ( 3 sec) [ -1001.5477] [Branch lengths ] . ( 3 sec) [ -1001.4697] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.244362] . ( 3 sec) [ -1001.4118] [Branch lengths ] . ( 3 sec) [ -1001.3462] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.297115] . ( 4 sec) [ -1001.2930] [Branch lengths ] . ( 4 sec) [ -1001.2188] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.352689] . ( 4 sec) [ -1001.1640] [Branch lengths ] . ( 4 sec) [ -1001.1004] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.403609] . ( 4 sec) [ -1001.0492] [Branch lengths ] . ( 4 sec) [ -1000.9776] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.457180] . ( 4 sec) [ -1000.9250] [Branch lengths ] . ( 4 sec) [ -1000.8638] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.507091] . ( 4 sec) [ -1000.8124] [Branch lengths ] . ( 4 sec) [ -1000.7425] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.559978] . ( 4 sec) [ -1000.6897] [Branch lengths ] . ( 4 sec) [ -1000.6308] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.608110] . ( 5 sec) [ -1000.5814] [Branch lengths ] . ( 5 sec) [ -1000.5134] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.659413] . ( 5 sec) [ -1000.4626] [Branch lengths ] . ( 5 sec) [ -1000.4045] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.706446] . ( 5 sec) [ -1000.3568] [Branch lengths ] . ( 5 sec) [ -1000.2912] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.756076] . ( 5 sec) [ -1000.2426] [Branch lengths ] . ( 5 sec) [ -1000.1864] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.801670] . ( 5 sec) [ -1000.1405] [Branch lengths ] . ( 5 sec) [ -1000.0780] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.849459] . ( 5 sec) [ -1000.0316] [Branch lengths ] . ( 5 sec) [ -999.9784] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.893252] . ( 5 sec) [ -999.9347] [Branch lengths ] . ( 6 sec) [ -999.8750] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.939387] . ( 6 sec) [ -999.8310] [Branch lengths ] . ( 6 sec) [ -999.7802] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -2.981661] . ( 6 sec) [ -999.7389] [Branch lengths ] . ( 6 sec) [ -999.6824] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.025989] . ( 6 sec) [ -999.6410] [Branch lengths ] . ( 6 sec) [ -999.5933] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.066500] . ( 6 sec) [ -999.5546] [Branch lengths ] . ( 6 sec) [ -999.5016] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.108980] . ( 6 sec) [ -999.4628] [Branch lengths ] . ( 6 sec) [ -999.4183] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.147740] . ( 6 sec) [ -999.3823] [Branch lengths ] . ( 7 sec) [ -999.3329] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.188368] . ( 7 sec) [ -999.2969] [Branch lengths ] . ( 7 sec) [ -999.2556] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.225328] . ( 7 sec) [ -999.2222] [Branch lengths ] . ( 7 sec) [ -999.1769] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.263921] . ( 7 sec) [ -999.1437] [Branch lengths ] . ( 7 sec) [ -999.1055] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.299180] . ( 7 sec) [ -999.0747] [Branch lengths ] . ( 7 sec) [ -999.0334] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.335768] . ( 7 sec) [ -999.0030] [Branch lengths ] . ( 7 sec) [ -998.9679] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.369338] . ( 7 sec) [ -998.9397] [Branch lengths ] . ( 7 sec) [ -998.9022] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.403929] . ( 7 sec) [ -998.8745] [Branch lengths ] . ( 8 sec) [ -998.8424] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.435867] . ( 8 sec) [ -998.8167] [Branch lengths ] . ( 8 sec) [ -998.7824] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.467699] . ( 8 sec) [ -998.7591] [Branch lengths ] . ( 8 sec) [ -998.7302] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.496847] . ( 8 sec) [ -998.7085] [Branch lengths ] . ( 8 sec) [ -998.6777] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.526856] . ( 8 sec) [ -998.6567] [Branch lengths ] . ( 8 sec) [ -998.6305] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.554429] . ( 8 sec) [ -998.6109] [Branch lengths ] . ( 8 sec) [ -998.5829] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.582891] . ( 8 sec) [ -998.5639] [Branch lengths ] . ( 8 sec) [ -998.5402] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.608982] . ( 9 sec) [ -998.5226] [Branch lengths ] . ( 9 sec) [ -998.4973] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.635854] . ( 9 sec) [ -998.4803] [Branch lengths ] . ( 9 sec) [ -998.4587] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.660605] . ( 9 sec) [ -998.4430] [Branch lengths ] . ( 9 sec) [ -998.4201] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.686042] . ( 9 sec) [ -998.4048] [Branch lengths ] . ( 9 sec) [ -998.3855] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.709387] . ( 9 sec) [ -998.3713] [Branch lengths ] . ( 9 sec) [ -998.3508] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.733391] . ( 9 sec) [ -998.3371] [Branch lengths ] . ( 9 sec) [ -998.3197] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.755417] . ( 10 sec) [ -998.3071] [Branch lengths ] . ( 10 sec) [ -998.2887] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.778027] . ( 10 sec) [ -998.2765] [Branch lengths ] . ( 10 sec) [ -998.2609] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.798807] . ( 10 sec) [ -998.2495] [Branch lengths ] . ( 10 sec) [ -998.2334] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.819929] . ( 10 sec) [ -998.2225] [Branch lengths ] . ( 10 sec) [ -998.2085] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.839467] . ( 10 sec) [ -998.1984] [Branch lengths ] . ( 10 sec) [ -998.1839] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.859352] . ( 10 sec) [ -998.1742] [Branch lengths ] . ( 10 sec) [ -998.1618] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.877731] . ( 11 sec) [ -998.1527] [Branch lengths ] . ( 11 sec) [ -998.1398] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.896500] . ( 11 sec) [ -998.1311] [Branch lengths ] . ( 11 sec) [ -998.1199] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.913883] . ( 11 sec) [ -998.1118] [Branch lengths ] . ( 11 sec) [ -998.1002] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.931641] . ( 11 sec) [ -998.0924] [Branch lengths ] . ( 11 sec) [ -998.0824] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.948040] . ( 11 sec) [ -998.0752] [Branch lengths ] . ( 11 sec) [ -998.0648] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.964802] . ( 11 sec) [ -998.0578] [Branch lengths ] . ( 11 sec) [ -998.0489] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.980276] . ( 12 sec) [ -998.0424] [Branch lengths ] . ( 12 sec) [ -998.0330] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -3.996108] . ( 12 sec) [ -998.0268] [Branch lengths ] . ( 12 sec) [ -998.0188] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.010728] . ( 12 sec) [ -998.0130] [Branch lengths ] . ( 12 sec) [ -998.0046] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.025672] . ( 12 sec) [ -997.9990] [Branch lengths ] . ( 12 sec) [ -997.9919] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.039476] . ( 12 sec) [ -997.9867] [Branch lengths ] . ( 12 sec) [ -997.9792] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.053592] . ( 12 sec) [ -997.9742] [Branch lengths ] . ( 12 sec) [ -997.9677] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.066642] . ( 12 sec) [ -997.9631] [Branch lengths ] . ( 13 sec) [ -997.9564] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.079984] . ( 13 sec) [ -997.9519] [Branch lengths ] . ( 13 sec) [ -997.9461] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.092312] . ( 13 sec) [ -997.9419] [Branch lengths ] . ( 13 sec) [ -997.9359] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.104933] . ( 13 sec) [ -997.9319] [Branch lengths ] . ( 13 sec) [ -997.9267] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.116589] . ( 13 sec) [ -997.9229] [Branch lengths ] . ( 13 sec) [ -997.9175] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.128527] . ( 13 sec) [ -997.9139] [Branch lengths ] . ( 13 sec) [ -997.9093] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.139522] . ( 13 sec) [ -997.9059] [Branch lengths ] . ( 13 sec) [ -997.9010] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.150855] . ( 14 sec) [ -997.8978] [Branch lengths ] . ( 14 sec) [ -997.8936] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.161269] . ( 14 sec) [ -997.8906] [Branch lengths ] . ( 14 sec) [ -997.8861] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.172011] . ( 14 sec) [ -997.8832] [Branch lengths ] . ( 14 sec) [ -997.8795] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.181888] . ( 14 sec) [ -997.8767] [Branch lengths ] . ( 14 sec) [ -997.8727] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.192078] . ( 14 sec) [ -997.8701] [Branch lengths ] . ( 14 sec) [ -997.8667] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.201454] . ( 14 sec) [ -997.8642] [Branch lengths ] . ( 14 sec) [ -997.8606] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.211127] . ( 14 sec) [ -997.8582] [Branch lengths ] . ( 15 sec) [ -997.8552] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.220032] . ( 15 sec) [ -997.8530] [Branch lengths ] . ( 15 sec) [ -997.8497] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.229220] . ( 15 sec) [ -997.8475] [Branch lengths ] . ( 15 sec) [ -997.8448] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.237683] . ( 15 sec) [ -997.8428] [Branch lengths ] . ( 15 sec) [ -997.8399] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.244880] . ( 15 sec) [ -997.8387] [Branch lengths ] . ( 15 sec) [ -997.8364] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.251184] . ( 15 sec) [ -997.8353] [Branch lengths ] . ( 15 sec) [ -997.8328] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.257718] . ( 15 sec) [ -997.8317] [Branch lengths ] . ( 16 sec) [ -997.8296] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.263695] . ( 16 sec) [ -997.8286] [Branch lengths ] . ( 16 sec) [ -997.8264] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.269875] . ( 16 sec) [ -997.8254] [Branch lengths ] . ( 16 sec) [ -997.8233] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.278837] . ( 16 sec) [ -997.8209] [Branch lengths ] . ( 16 sec) [ -997.8185] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.286772] . ( 16 sec) [ -997.8169] [Branch lengths ] . ( 16 sec) [ -997.8150] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.293819] . ( 16 sec) [ -997.8150] [Selective constraints on amino acids ][0.385234 * aa_fitness[i,j] + -4.293819] . Log likelihood of the current tree: -997.814997. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Final values of parameters . Sequence filename: 20110203_155022.txt . Data type : codon . Sequence format : interleaved . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of codons substitution: /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11 . Number of taxa: 4 . Log-likelihood: -997.81500 . Unconstrained likelihood: -354.56409 . Parsimony: 208 . Tree size: 160.35797 . Discrete Selection: No . Selective constraints on amino acids: optimize? 0 1 : 0.385234 * aa_fitness[i,j] + -4.293819 . Scale parameter of Gamma distribution: optimize? 0 : 0.917608 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.307849 2.215535 1.010220 1.065729 1.085499 0.890831 transversion m_[tc][ag] 0.307849 transition/transversion m_tc|ag / m_[tc][ag] 2.215535 T <-> C / transition m_tc / m_tc|ag 0.989780 A <-> G / transition m_ag / m_tc|ag 1.010220 T <-> C / transversion m_tc / m_[tc][ag] 2.192892 A <-> G / transversion m_ag / m_[tc][ag] 2.238178 T <-> A / transversion m_ta / m_[tc][ag] 1.065729 T <-> G / transversion m_tg / m_[tc][ag] 1.085499 C <-> A / transversion m_ca / m_[tc][ag] 0.890831 C <-> G / transversion m_cg / m_[tc][ag] 0.957941 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.268305 0.195920 0.239202 0.296573 - f(A) = 0.268305 - f(C) = 0.195920 - f(G) = 0.239202 - f(T) = 0.296573 . Codon frequencies: from_sequence? 1 : TTT F 0.017102 TTC F 0.020188 TTA L 0.010929 TTG L 0.010929 TCT S 0.014015 TCC S 0.010929 TCA S 0.017102 TCG S 0.010929 TAT Y 0.023275 TAC Y 0.017102 TAA * 0.000000 TAG * 0.000000 TGT C 0.001670 TGC C 0.001670 TGA * 0.000000 TGG W 0.023275 CTT L 0.007843 CTC L 0.004756 CTA L 0.014015 CTG L 0.004756 CCT P 0.020188 CCC P 0.010929 CCA P 0.007843 CCG P 0.007843 CAT H 0.004756 CAC H 0.001670 CAA Q 0.014015 CAG Q 0.014015 CGT R 0.010929 CGC R 0.014015 CGA R 0.014015 CGG R 0.010929 ATT I 0.007843 ATC I 0.010929 ATA I 0.007843 ATG M 0.029447 ACT T 0.004756 ACC T 0.007843 ACA T 0.001670 ACG T 0.001670 AAT N 0.041793 AAC N 0.007843 AAA K 0.060312 AAG K 0.075744 AGT S 0.020188 AGC S 0.010929 AGA R 0.010929 AGG R 0.004756 GTT V 0.007843 GTC V 0.007843 GTA V 0.007843 GTG V 0.014015 GCT A 0.032534 GCC A 0.026361 GCA A 0.026361 GCG A 0.032534 GAT D 0.017102 GAC D 0.026361 GAA E 0.051052 GAG E 0.057225 GGT G 0.014015 GGC G 0.010929 GGA G 0.007843 GGG G 0.014015 . Time used 0h0m16s . 16 seconds oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Suggested citation: S. Guindon & O. Gascuel "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood" Systematic Biology. 2003. 52(5):696-704. Modified for a codon model by Sanzo Miyazawa (sanzo.miyazawa@gmail.com) oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Printing the most likely tree in file '20110203_155022.txt_phyml_tree.txt'...