Relaxed phylogenetics and dating with Anonymous sex chat with a bot
It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. However, the clock models in BEAST - which are discussed on this page - may also be used when analysing contemporaneous sequences.
In Bayesian clock dating, priors on times and rates are combined with the likelihood (the probability of the sequence data) to produce the posterior of times and rates. Statistical inference methodologies in which statistical distributions are used to represent uncertainties in model parameters. They are established through fossil-based minimum and maximum constraints on clade ages (node calibrations) or through the inclusion of dated fossil species in the analysis (tip calibrations).The figure above shows 2 fixed local clocks: a first one for the clade defined by viruses 1 through 4 and a second one for the clade defined by viruses 6 and 7. BEAST estimates that the former has a high evolutionary rate and the latter has a low evolutionary rate, with those rates being constant within each clade.
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Random local clocks permit an amount of variation in evolutionary rate across a tree which is more than the strict clock (which has no variation) but less than the relaxed clock (which has a different rate for each branch) (Drummond and Suchard, 2010). Suchard (2008) Bayesian analysis of elapsed times in continuous‐time Markov chains.