oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 3.3.20211231 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Sequence filename: raytAln.phy . Data set: #1 . Initial tree: BioNJ . Model of nucleotides substitution: GTR . Number of taxa: 138 . Log-likelihood: -12656.76238 . Unconstrained log-likelihood: -2758.11258 . Composite log-likelihood: -90480.93534 . Parsimony: 2753 . Tree size: 9.60355 . Discrete gamma model: Yes - Number of classes: 4 - Gamma shape parameter: 0.732 - Relative rate in class 1: 0.08094 [freq=0.250000] - Relative rate in class 2: 0.37804 [freq=0.250000] - Relative rate in class 3: 0.93602 [freq=0.250000] - Relative rate in class 4: 2.60500 [freq=0.250000] . Nucleotides frequencies: - f(A)= 0.18381 - f(C)= 0.30992 - f(G)= 0.30238 - f(T)= 0.20388 . GTR relative rate parameters : A <-> C 1.33496 A <-> G 3.82744 A <-> T 1.21065 C <-> G 1.14506 C <-> T 3.79130 G <-> T 1.00000 . Instantaneous rate matrix : [A---------C---------G---------T------] -1.22388 0.27854 0.77916 0.16618 0.16520 -0.91871 0.23310 0.52040 0.47365 0.23892 -0.84983 0.13726 0.14982 0.79106 0.20357 -1.14445 . Run ID: none . Random seed: 1692143732 . Subtree patterns aliasing: no . Version: 3.3.20211231 . Time used: 0h1m37s (97 seconds) oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Suggested citations: S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0." Systematic Biology. 2010. 59(3):307-321. S. Guindon & O. Gascuel "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood" Systematic Biology. 2003. 52(5):696-704. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo