Blog Archives

PhyloTempo

May 14, 2013
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PhyloTempo

Summary: Two new measures of tree topology are introduced: temporal clustering (TC), and staircase-ness. Several other existing statistics are also implemented for the purpose of comparison: Aldous's graphical test and likelihood test to decide if a tree fits the Yule … Continue reading →

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Clustering using dynamic tree cut

February 3, 2013
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Clustering using dynamic tree cut

Summary: Two methods for hierarchical clustering are introduced: (i) dynamic tree cut; and (ii) dynamic hybrid cut. Dynamic tree cut is a top-down algorithm that relies solely on the dendrogram. The algorithm implements an adaptive, iterative process of cluster decomposition … Continue reading →

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Population dynamics using INLA

December 5, 2012
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Population dynamics using INLA

Summary: Two methods of inferring (effective) population dynamics from genetic variation are compared: (i) Markov chain Monte Carlo (MCMC; using BEAST); and (ii) integrated nested Laplace approximation (INLA; using R interface of that name). INLA runs >1000 times faster than … Continue reading →

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