Selected article for: "maximum likelihood and time reversible"
Author: Maciej F Boni; Philippe Lemey; Xiaowei Jiang; Tommy Tsan-Yuk Lam; Blair Perry; Todd Castoe; Andrew Rambaut; David L Robertson
Title: Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
  • Document date: 2020_3_31
    • ID: h2uc7ria_49
    Snippet: We focused on these three non-recombining regions/alignments for divergence time estimation. This avoids inappropriately modelling evolutionary processes with recombination on strictly bifurcating trees, which can result in different artefacts such as homoplasies that inflate branch lengths and result in apparently longer evolutionary divergence times. In order to examine temporal signal in the sequenced data, we plotted root-totip divergence aga.....
    Document: We focused on these three non-recombining regions/alignments for divergence time estimation. This avoids inappropriately modelling evolutionary processes with recombination on strictly bifurcating trees, which can result in different artefacts such as homoplasies that inflate branch lengths and result in apparently longer evolutionary divergence times. In order to examine temporal signal in the sequenced data, we plotted root-totip divergence against sampling time using TempEst based on a maximum likelihood tree. The latter was reconstructed using IQTREE (Nguyen et al., 2014 ) under a General-Time Reversible (GTR) model with a discrete gamma distribution to model among-site rate variation.

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