The conditioned reconstructed process
Citations
18,718 citations
Cites background or methods from "The conditioned reconstructed proce..."
...…prior model on clock trees has been expanded to incorporate recent progress in the understanding of the linear constant birth–death process with complete sampling (Gernhard 2008), with random incomplete sampling (Stadler 2009), or with clustered or diversified sampling (Höhna et al. 2011)....
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...The birth–death prior model on clock trees has been expanded to incorporate recent progress in the understanding of the linear constant birth–death process with complete sampling (Gernhard 2008), with random incomplete sampling (Stadler 2009), or with clustered or diversified sampling (Höhna et al....
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2,401 citations
Cites methods from "The conditioned reconstructed proce..."
...For the divergence times, we use the reconstructed birth–death process (Gernhard 2008), parameterized by lineage birth and death rates λ and μ:...
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...For the divergence times, we use the reconstructed birth–death process (Gernhard 2008), parameterized by lineage birth and death rates λ and µ: fBD(S ) = ns!λ ns−1(λ− µ) e −(λ−µ)x1 λ− µ e−(λ−µ)x1 × ns−1∏ i=1 (λ− µ)2 e−(λ−µ)xi λ− µ e−(λ−µ)xi , (5) where ns is the number of species and x1, x2, . . .…...
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...One hundred species trees were simulated using a birth– death process with λ = 1 and µ = 0.2 (Gernhard 2008)....
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...…on a popular existing software package for Bayesian phylogenetics, and as a result it can exploit existing models for gene trees such as relaxed molecular clocks (Drummond et al. 2006) and previously implemented priors for species tree such as the reconstructed birth–death prior (Gernhard 2008)....
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...2006) and previously implemented priors for species tree such as the reconstructed birth–death prior (Gernhard 2008)....
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588 citations
Cites methods from "The conditioned reconstructed proce..."
...For all analyses using calibration priors (fixed-scaled, fixed-true, and hyperprior), we assumed a constant-rate reconstructed birth-death process [39, 40] as a prior on speciation times....
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556 citations
421 citations
Cites methods from "The conditioned reconstructed proce..."
...A Birth-Death tree prior was used, which accounts for both speciation and extinction [110]....
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References
16,450 citations
"The conditioned reconstructed proce..." refers methods in this paper
...We investigate the constant rate birth-death process (Feller, 1968; Kendall, 1948) as it is probably the most popular homogeneous model....
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1,564 citations
1,508 citations
"The conditioned reconstructed proce..." refers background in this paper
...For the general birth-death process, the joint probability for the shape and all speciation times has been established in Rannala and Yang (1996); the joint probability for the speciation times disregarding the shape has been established in Yang and Rannala (1997)....
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...In Rannala and Yang (1996), joint probabilities for x1, . . . , xn−1 are given....
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...Rannala and Yang (1996) ; the joint probability for the speciation times disregarding...
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1,230 citations
"The conditioned reconstructed proce..." refers background or methods in this paper
...From Yang and Rannala (1997), Equation (3), we obtain the density g of the ordered speciation times, x2 > x3 > . . . > xn−1, given n and x1 = t1, g(x2, x3, . . . , xn|t1 = t, n) = (n − 2)! n−1 ∏ i=2 µ p1(xi) p0(t) ....
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...For the general birth-death process, the joint probability for the shape and all speciation times has been established in Rannala and Yang (1996); the joint probability for the speciation times disregarding the shape has been established in Yang and Rannala (1997)....
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...This joint density is used in Yang and Rannala (1997) in order to infer reconstructed trees with Bayesian methods....
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