P A U P * Version 4.0b10 for 32-bit Microsoft Windows Thu May 07 15:28:20 2009 -----------------------------NOTICE----------------------------- This is a beta-test version. Please report any crashes, apparent calculation errors, or other anomalous results. There are no restrictions on publication of results obtained with this version, but you should check the WWW site frequently for bug announcements and/or updated versions. See the README file on the distribution media for details. ---------------------------------------------------------------- Neighbor-joining search settings: Ties (if encountered) will be broken randomly; initial seed = 0 Distance measure = Jukes-Cantor (Tree is unrooted) Note: Ties were encountered; neighbor-joining tree may not be unique Tree found by neighbor-joining method stored in tree buffer Time used = 0.00 sec ***** BEGIN TESTING 56 MODELS OF EVOLUTION ***** Optimality criterion set to likelihood. ** Model 1 of 56 * Calculating JC ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to the JC69 model Number of distinct data patterns under this model = 97 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2696.87912 Time used to compute likelihoods = 0.03 sec ** Model 2 of 56 * Calculating JC+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to the JC69+I model Number of distinct data patterns under this model = 97 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2620.85717 Estimated value of proportion of invariable sites = 0.728917 Time used to compute likelihoods = 0.52 sec ** Model 3 of 56 * Calculating JC+GÊ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the JC69+G model Number of distinct data patterns under this model = 97 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2618.22607 Estimated value of gamma shape parameter = 0.162541 Time used to compute likelihoods = 0.80 sec ** Model 4 of 56 * Calculating JC+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the JC69+G+I model Number of distinct data patterns under this model = 97 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2612.83649 Estimated value of proportion of invariable sites = 0.530319 Estimated value of gamma shape parameter = 0.682833 Time used to compute likelihoods = 6.30 sec ** Model 5 of 56 * Calculating F81 ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to the F81 model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2673.25292 Estimated base frequencies = A:0.209795 C:0.302719 G:0.302740 T:0.184746 Time used to compute likelihoods = 1.63 sec ** Model 6 of 56 * Calculating F81+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to the F81+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2593.57034 Estimated base frequencies = A:0.202841 C:0.315951 G:0.298485 T:0.182723 Estimated value of proportion of invariable sites = 0.734283 Time used to compute likelihoods = 7.64 sec ** Model 7 of 56 * Calculating F81+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the F81+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2591.36515 Estimated base frequencies = A:0.203464 C:0.314547 G:0.299075 T:0.182915 Estimated value of gamma shape parameter = 0.152168 Time used to compute likelihoods = 9.28 sec ** Model 8 of 56 * Calculating F81+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 1 Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the F81+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2585.88629 Estimated base frequencies = A:0.203250 C:0.315392 G:0.298538 T:0.182820 Estimated value of proportion of invariable sites = 0.540339 Estimated value of gamma shape parameter = 0.683076 Time used to compute likelihoods = 13.30 sec ** Model 9 of 56 * Calculating K80 ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 Transition/transversion ratio estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to the K80(K2P) model Number of distinct data patterns under this model = 111 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2635.81719 Estimated ti/tv ratio = 2.161068 (kappa = 4.322136) Time used to compute likelihoods = 0.13 sec ** Model 10 of 56 * Calculating K80+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 Transition/transversion ratio estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to the K80(K2P)+I model Number of distinct data patterns under this model = 111 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2556.95900 Estimated ti/tv ratio = 2.316615 (kappa = 4.633230) Estimated value of proportion of invariable sites = 0.732596 Time used to compute likelihoods = 5.24 sec ** Model 11 of 56 * Calculating K80+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 Transition/transversion ratio estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the K80(K2P)+G model Number of distinct data patterns under this model = 111 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2554.38702 Estimated ti/tv ratio = 2.311614 (kappa = 4.623228) Estimated value of gamma shape parameter = 0.157502 Time used to compute likelihoods = 6.14 sec ** Model 12 of 56 * Calculating K80+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 Transition/transversion ratio estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the K80(K2P)+G+I model Number of distinct data patterns under this model = 111 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2548.50031 Estimated ti/tv ratio = 2.352914 (kappa = 4.705827) Estimated value of proportion of invariable sites = 0.537764 Estimated value of gamma shape parameter = 0.669945 Time used to compute likelihoods = 7.64 sec ** Model 13 of 56 * Calculating HKY ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to the HKY85 model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2606.20867 Estimated base frequencies = A:0.199566 C:0.318455 G:0.300989 T:0.180989 Estimated ti/tv ratio = 2.201937 (kappa = 4.676834) Time used to compute likelihoods = 1.74 sec ** Model 14 of 56 * Calculating HKY+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to the HKY85+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2515.89691 Estimated base frequencies = A:0.196857 C:0.329527 G:0.313765 T:0.159851 Estimated ti/tv ratio = 2.596611 (kappa = 5.669765) Estimated value of proportion of invariable sites = 0.746286 Time used to compute likelihoods = 10.13 sec ** Model 15 of 56 * Calculating HKY+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2514.47843 Estimated base frequencies = A:0.196703 C:0.329214 G:0.313048 T:0.161035 Estimated ti/tv ratio = 2.572909 (kappa = 5.611041) Estimated value of gamma shape parameter = 0.127865 Time used to compute likelihoods = 16.34 sec ** Model 16 of 56 * Calculating HKY+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the HKY85+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2508.44817 Estimated base frequencies = A:0.197607 C:0.328421 G:0.312742 T:0.161230 Estimated ti/tv ratio = 2.627797 (kappa = 5.722536) Estimated value of proportion of invariable sites = 0.564684 Estimated value of gamma shape parameter = 0.661861 Time used to compute likelihoods = 19.64 sec ** Model 17 of 56 * Calculating TrNef ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2612.07650 Estimated R-matrix: - 1 2.2499445 1 1 - 1 6.910571 2.2499445 1 - 1 1 6.910571 1 - Time used to compute likelihoods = 1.89 sec ** Model 18 of 56 * Calculating TrNef+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2546.74987 Estimated R-matrix: - 1 2.6453052 1 1 - 1 6.5826493 2.6453052 1 - 1 1 6.5826493 1 - Estimated value of proportion of invariable sites = 0.700329 Time used to compute likelihoods = 5.19 sec ** Model 19 of 56 * Calculating TrNef+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2541.56044 Estimated R-matrix: - 1 2.5015522 1 1 - 1 7.0226847 2.5015522 1 - 1 1 7.0226847 1 - Estimated value of gamma shape parameter = 0.210555 Time used to compute likelihoods = 7.94 sec ** Model 20 of 56 * Calculating TrNef+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2536.29840 Estimated R-matrix: - 1 2.5562236 1 1 - 1 7.1192099 2.5562236 1 - 1 1 7.1192099 1 - Estimated value of proportion of invariable sites = 0.495935 Estimated value of gamma shape parameter = 0.685933 Time used to compute likelihoods = 8.97 sec ** Model 21 of 56 * Calculating TrN ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model (this is the TN93 model) Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2573.00939 Estimated base frequencies = A:0.226741 C:0.294122 G:0.328644 T:0.150493 Estimated R-matrix: - 1 2.0780589 1 1 - 1 8.9151026 2.0780589 1 - 1 1 8.9151026 1 - Time used to compute likelihoods = 2.78 sec ** Model 22 of 56 * Calculating TrN+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model (this is the TN93+I model) Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2496.44711 Estimated base frequencies = A:0.220810 C:0.312445 G:0.330539 T:0.136206 Estimated R-matrix: - 1 2.5002536 1 1 - 1 10.261295 2.5002536 1 - 1 1 10.261295 1 - Estimated value of proportion of invariable sites = 0.703526 Time used to compute likelihoods = 7.69 sec ** Model 23 of 56 * Calculating TrN+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model (this is the TN93+G model) Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2491.96001 Estimated base frequencies = A:0.222006 C:0.310724 G:0.331672 T:0.135598 Estimated R-matrix: - 1 2.3525465 1 1 - 1 10.909415 2.3525465 1 - 1 1 10.909415 1 - Estimated value of gamma shape parameter = 0.188520 Time used to compute likelihoods = 10.03 sec ** Model 24 of 56 * Calculating TrN+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b a C a - a e G b a - a T a e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model (this is the TN93+G+I model) Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2486.77857 Estimated base frequencies = A:0.221628 C:0.309960 G:0.331967 T:0.136445 Estimated R-matrix: - 1 2.3960658 1 1 - 1 11.148534 2.3960658 1 - 1 1 11.148534 1 - Estimated value of proportion of invariable sites = 0.528310 Estimated value of gamma shape parameter = 0.738984 Time used to compute likelihoods = 16.91 sec ** Model 25 of 56 * Calculating K3P ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2635.76248 Estimated R-matrix: - 1 4.496177 1.0810259 1 - 1.0810259 4.496177 4.496177 1.0810259 - 1 1.0810259 4.496177 1 - Time used to compute likelihoods = 1.52 sec ** Model 26 of 56 * Calculating K3P+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2556.92079 Estimated R-matrix: - 1 4.8026927 1.0737154 1 - 1.0737154 4.8026927 4.8026927 1.0737154 - 1 1.0737154 4.8026927 1 - Estimated value of proportion of invariable sites = 0.732579 Time used to compute likelihoods = 3.77 sec ** Model 27 of 56 * Calculating K3P+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2554.35219 Estimated R-matrix: - 1 4.7834463 1.0699101 1 - 1.0699101 4.7834463 4.7834463 1.0699101 - 1 1.0699101 4.7834463 1 - Estimated value of gamma shape parameter = 0.157484 Time used to compute likelihoods = 5.91 sec ** Model 28 of 56 * Calculating K3P+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2548.47968 Estimated R-matrix: - 1 4.8326487 1.0546365 1 - 1.0546365 4.8326487 4.8326487 1.0546365 - 1 1.0546365 4.8326487 1 - Estimated value of proportion of invariable sites = 0.537476 Estimated value of gamma shape parameter = 0.669352 Time used to compute likelihoods = 8.73 sec ** Model 29 of 56 * Calculating K3Puf ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2606.17316 Estimated base frequencies = A:0.199380 C:0.318576 G:0.301186 T:0.180857 Estimated R-matrix: - 1 4.5261524 0.93882455 1 - 0.93882455 4.5261524 4.5261524 0.93882455 - 1 0.93882455 4.5261524 1 - Time used to compute likelihoods = 1.55 sec ** Model 30 of 56 * Calculating K3Puf+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2515.47738 Estimated base frequencies = A:0.195293 C:0.330175 G:0.315401 T:0.159130 Estimated R-matrix: - 1 4.9941122 0.78112033 1 - 0.78112033 4.9941122 4.9941122 0.78112033 - 1 0.78112033 4.9941122 1 - Estimated value of proportion of invariable sites = 0.746479 Time used to compute likelihoods = 14.06 sec ** Model 31 of 56 * Calculating K3Puf+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2514.06940 Estimated base frequencies = A:0.195154 C:0.329916 G:0.314675 T:0.160255 Estimated R-matrix: - 1 4.9584327 0.78475703 1 - 0.78475703 4.9584327 4.9584327 0.78475703 - 1 0.78475703 4.9584327 1 - Estimated value of gamma shape parameter = 0.127174 Time used to compute likelihoods = 10.17 sec ** Model 32 of 56 * Calculating K3Puf+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 3 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c b G b c - a T c b a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2508.00594 Estimated base frequencies = A:0.196029 C:0.329136 G:0.314387 T:0.160448 Estimated R-matrix: - 1 5.0253406 0.77267686 1 - 0.77267686 5.0253406 5.0253406 0.77267686 - 1 0.77267686 5.0253406 1 - Estimated value of proportion of invariable sites = 0.567122 Estimated value of gamma shape parameter = 0.666185 Time used to compute likelihoods = 16.41 sec ** Model 33 of 56 * Calculating TIMef ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2612.01459 Estimated R-matrix: - 1 2.3466555 1.086172 1 - 1.086172 7.2079875 2.3466555 1.086172 - 1 1.086172 7.2079875 1 - Time used to compute likelihoods = 1.34 sec ** Model 34 of 56 * Calculating TIMef+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2546.70168 Estimated R-matrix: - 1 2.7526009 1.0817119 1 - 1.0817119 6.8510511 2.7526009 1.0817119 - 1 1.0817119 6.8510511 1 - Estimated value of proportion of invariable sites = 0.700295 Time used to compute likelihoods = 6.49 sec ** Model 35 of 56 * Calculating TIMef+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2541.51854 Estimated R-matrix: - 1 2.5961938 1.0761681 1 - 1.0761681 7.2886403 2.5961938 1.0761681 - 1 1.0761681 7.2886403 1 - Estimated value of gamma shape parameter = 0.210554 Time used to compute likelihoods = 7.34 sec ** Model 36 of 56 * Calculating TIMef+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2536.27207 Estimated R-matrix: - 1 2.6338772 1.0614354 1 - 1.0614354 7.3354339 2.6338772 1.0614354 - 1 1.0614354 7.3354339 1 - Estimated value of proportion of invariable sites = 0.495624 Estimated value of gamma shape parameter = 0.685494 Time used to compute likelihoods = 13.84 sec ** Model 37 of 56 * Calculating TIM ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2572.96023 Estimated base frequencies = A:0.226653 C:0.292953 G:0.328667 T:0.151728 Estimated R-matrix: - 1 2.0127365 0.94175642 1 - 0.94175642 8.6046212 2.0127365 0.94175642 - 1 0.94175642 8.6046212 1 - Time used to compute likelihoods = 2.11 sec ** Model 38 of 56 * Calculating TIM+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2496.19751 Estimated base frequencies = A:0.219515 C:0.312833 G:0.331752 T:0.135901 Estimated R-matrix: - 1 2.273498 0.82981129 1 - 0.82981129 9.2911995 2.273498 0.82981129 - 1 0.82981129 9.2911995 1 - Estimated value of proportion of invariable sites = 0.703867 Time used to compute likelihoods = 9.23 sec ** Model 39 of 56 * Calculating TIM+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2491.69965 Estimated base frequencies = A:0.220740 C:0.311196 G:0.332874 T:0.135190 Estimated R-matrix: - 1 2.1345138 0.8263052 1 - 0.8263052 9.8751547 2.1345138 0.8263052 - 1 0.8263052 9.8751547 1 - Estimated value of gamma shape parameter = 0.187820 Time used to compute likelihoods = 15.14 sec ** Model 40 of 56 * Calculating TIM+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 4 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - c e G b c - a T c e a - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2486.46892 Estimated base frequencies = A:0.220249 C:0.310448 G:0.333287 T:0.136016 Estimated R-matrix: - 1 2.1508525 0.80772797 1 - 0.80772797 9.9876104 2.1508525 0.80772797 - 1 0.80772797 9.9876104 1 - Estimated value of proportion of invariable sites = 0.530093 Estimated value of gamma shape parameter = 0.740764 Time used to compute likelihoods = 16.34 sec ** Model 41 of 56 * Calculating TVMef ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2626.43638 Estimated R-matrix: - 0.95721383 4.3910613 0.199318 0.95721383 - 1.5488685 4.3910613 4.3910613 1.5488685 - 1 0.199318 4.3910613 1 - Time used to compute likelihoods = 1.59 sec ** Model 42 of 56 * Calculating TVMef+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2549.93117 Estimated R-matrix: - 0.74591183 4.0011688 0.14219134 0.74591183 - 1.2276715 4.0011688 4.0011688 1.2276715 - 1 0.14219134 4.0011688 1 - Estimated value of proportion of invariable sites = 0.728412 Time used to compute likelihoods = 9.75 sec ** Model 43 of 56 * Calculating TVMef+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2546.88428 Estimated R-matrix: - 0.77160063 4.0792656 0.14091518 0.77160063 - 1.2810384 4.0792656 4.0792656 1.2810384 - 1 0.14091518 4.0792656 1 - Estimated value of gamma shape parameter = 0.165842 Time used to compute likelihoods = 9.45 sec ** Model 44 of 56 * Calculating TVMef+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2540.86935 Estimated R-matrix: - 0.76449637 4.1036618 0.12460086 0.76449637 - 1.2722853 4.1036618 4.1036618 1.2722853 - 1 0.12460086 4.1036618 1 - Estimated value of proportion of invariable sites = 0.530952 Estimated value of gamma shape parameter = 0.661924 Time used to compute likelihoods = 13.98 sec ** Model 45 of 56 * Calculating TVM ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2601.30461 Estimated base frequencies = A:0.203072 C:0.315478 G:0.297180 T:0.184270 Estimated R-matrix: - 0.80967923 4.0232286 0.21882701 0.80967923 - 1.0611962 4.0232286 4.0232286 1.0611962 - 1 0.21882701 4.0232286 1 - Time used to compute likelihoods = 3.03 sec ** Model 46 of 56 * Calculating TVM+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2512.91849 Estimated base frequencies = A:0.201097 C:0.330169 G:0.309388 T:0.159346 Estimated R-matrix: - 0.6358661 3.797661 0.15691329 0.6358661 - 0.68428698 3.797661 3.797661 0.68428698 - 1 0.15691329 3.797661 1 - Estimated value of proportion of invariable sites = 0.746613 Time used to compute likelihoods = 17.11 sec ** Model 47 of 56 * Calculating TVM+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2511.50997 Estimated base frequencies = A:0.201252 C:0.329728 G:0.308241 T:0.160779 Estimated R-matrix: - 0.64055045 3.8002042 0.17014035 0.64055045 - 0.70059889 3.8002042 3.8002042 0.70059889 - 1 0.17014035 3.8002042 1 - Estimated value of gamma shape parameter = 0.128412 Time used to compute likelihoods = 16.47 sec ** Model 48 of 56 * Calculating TVM+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 5 (restriction of 6ST GTR model) Substitution classification: A C G T A - a b c C a - d b G b d - e T c b e - Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2505.39389 Estimated base frequencies = A:0.202446 C:0.328745 G:0.307717 T:0.161092 Estimated R-matrix: - 0.63632682 3.8567444 0.16686464 0.63632682 - 0.69871259 3.8567444 3.8567444 0.69871259 - 1 0.16686464 3.8567444 1 - Estimated value of proportion of invariable sites = 0.564738 Estimated value of gamma shape parameter = 0.662987 Time used to compute likelihoods = 27.92 sec ** Model 49 of 56 * Calculating SYM ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2602.61381 Estimated R-matrix: - 0.9726797 2.3151325 0.19955147 0.9726797 - 1.5659883 7.1125744 2.3151325 1.5659883 - 1 0.19955147 7.1125744 1 - Time used to compute likelihoods = 1.72 sec ** Model 50 of 56 * Calculating SYM+I ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to a submodel of the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2539.11785 Estimated R-matrix: - 0.83598895 2.4238931 0.15154883 0.83598895 - 1.3487173 6.170313 2.4238931 1.3487173 - 1 0.15154883 6.170313 1 - Estimated value of proportion of invariable sites = 0.694156 Time used to compute likelihoods = 10.23 sec ** Model 51 of 56 * Calculating SYM+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2533.32248 Estimated R-matrix: - 0.90511055 2.3959979 0.14645986 0.90511055 - 1.4469394 6.8997405 2.3959979 1.4469394 - 1 0.14645986 6.8997405 1 - Estimated value of gamma shape parameter = 0.219225 Time used to compute likelihoods = 10.64 sec ** Model 52 of 56 * Calculating SYM+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Assumed nucleotide frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to a submodel of the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2528.13828 Estimated R-matrix: - 0.90568761 2.4274041 0.13032134 0.90568761 - 1.4313894 6.9170912 2.4274041 1.4313894 - 1 0.13032134 6.9170912 1 - Estimated value of proportion of invariable sites = 0.485103 Estimated value of gamma shape parameter = 0.672861 Time used to compute likelihoods = 20.39 sec ** Model 53 of 56 * Calculating GTR ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal These settings correspond to the GTR model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2568.18067 Estimated base frequencies = A:0.231785 C:0.291002 G:0.323356 T:0.153856 Estimated R-matrix: - 0.74880572 1.7059765 0.21395209 0.74880572 - 0.99846016 7.2851787 1.7059765 0.99846016 - 1 0.21395209 7.2851787 1 - Time used to compute likelihoods = 4.58 sec ** Model 54 of 56 * Calculating GTR+IÊ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = equal These settings correspond to the GTR+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2492.71609 Estimated base frequencies = A:0.226410 C:0.313078 G:0.325485 T:0.135028 Estimated R-matrix: - 0.5474454 1.531549 0.15688915 0.5474454 - 0.64653493 6.4607956 1.531549 0.64653493 - 1 0.15688915 6.4607956 1 - Estimated value of proportion of invariable sites = 0.702257 Time used to compute likelihoods = 17.92 sec ** Model 55 of 56 * Calculating GTR+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the GTR+G model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2488.21554 Estimated base frequencies = A:0.227475 C:0.311575 G:0.326657 T:0.134293 Estimated R-matrix: - 0.54101628 1.4360472 0.1679702 0.54101628 - 0.64157155 6.8304409 1.4360472 0.64157155 - 1 0.1679702 6.8304409 1 - Estimated value of gamma shape parameter = 0.189207 Time used to compute likelihoods = 19.55 sec ** Model 56 of 56 * Calculating GTR+I+G ** Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 6 Substitution rate-matrix parameters estimated via ML Nucleotide frequencies estimated via ML Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean These settings correspond to the GTR+G+I model Number of distinct data patterns under this model = 144 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-006 -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities Writing likelihood scores (and parameter estimates) to file "C:\Documents and Settings\Lucie Vincent\Bureau\TP Phylo Venam\model.scores" Tree number 1: -Ln likelihood = 2483.09812 Estimated base frequencies = A:0.227063 C:0.310795 G:0.326973 T:0.135169 Estimated R-matrix: - 0.54422688 1.4541727 0.16552697 0.54422688 - 0.63015078 6.9354782 1.4541727 0.63015078 - 1 0.16552697 6.9354782 1 - Estimated value of proportion of invariable sites = 0.529415 Estimated value of gamma shape parameter = 0.749613 Time used to compute likelihoods = 29.22 sec