Selected article for: "time reversible model and variation rate"
Author: Zhizhou Tan; Gabriel Gonzalez; Jinliang Sheng; Jianmin Wu; Fuqiang Zhang; Lin Xu; Peisheng Zhang; Aiwei Zhu; Yonggang Qu; Changchun Tu; Michael J. Carr; Biao He
Title: Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events
  • Document date: 2019_5_3
    • ID: kcimb10m_26
    Snippet: The tMRCA for hosts and viral samples were estimated with Bayesian analyses conducted as 625 4 independent MCMC chains of 10 million generations each, sampled every 1,000 generations 626 (BEAST v2.4.6 [75] ). The cytb and LTAg gene multiple sequence alignments were used to infer 627 the divergence times among hosts and PyVs, respectively. The general time-reversible 628 substitution model with gamma-distributed rate variation across sites and a p.....
    Document: The tMRCA for hosts and viral samples were estimated with Bayesian analyses conducted as 625 4 independent MCMC chains of 10 million generations each, sampled every 1,000 generations 626 (BEAST v2.4.6 [75] ). The cytb and LTAg gene multiple sequence alignments were used to infer 627 the divergence times among hosts and PyVs, respectively. The general time-reversible 628 substitution model with gamma-distributed rate variation across sites and a proportion of 629 invariable sites (GTR+G+I) were assumed for both models. Other settings were: uncorrelated 630 lognormal relaxed molecular clocks for host and PyV models with a Bayesian skyline population 631 and exponential population models, respectively. These models chosen had the highest likelihood 632 when compared to other models with the PathSampler application in BEAST v2.4.6 package. The 633 host model was calibrated with divergence times between genera as inferred by Agnarsson [40] 634 and the PyV model was calibrated following Buck et al. [17, 76] .

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