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  "Title": "MCMC Algorithms for the Coalescent",
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      "title": "Run MCMC for Coalescent Trees",
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        "AIC.coalescentMCMC",
        "anova.coalescentMCMC",
        "BIC.coalescentMCMC",
        "coalescentMCMC",
        "logLik.coalescentMCMC"
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      "page": "dcoal",
      "title": "Density Functions of Some Time-Dependent Coalescent Models",
      "topics": [
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        "dcoal.linear",
        "dcoal.step",
        "dcoal.time",
        "dcoal.time2"
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        "getMCMCtrees",
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