phylodyn

phylodyn is an R tool package to estimate effective population size fluctuations over time using nonparametric Bayesian. The phylodyn algorithm uses the Markov chain Monte Carlo (MCMC) method and integrated nested Laplace (INLA) approximation for phylodynamic inference.

Topic

Phylogenetics;Genetics;Simulation experiment

Detail

  • Operation: Phylogenetic tree analysis

  • Software interface: Library

  • Language: R

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 0.9.02

  • Credit: NIH, EPSRC program grant, Enabling Quantification of Uncertainty in Inverse Problems, the DARPA funded program Enabling Quantification of Uncertainty in Physical Systems.

  • Input: -

  • Output: -

  • Contact: Michael D. Karcher mkarcher@uw.edu, Michael Karcher mkarcher@fredhutch.org

  • Collection: -

  • Maturity: Stable

Publications

  • phylodyn: an R package for phylodynamic simulation and inference.
  • Karcher MD, Palacios JA, Lan S, Minin VN. phylodyn: an R package for phylodynamic simulation and inference. Mol Ecol Resour. 2017 Jan;17(1):96-100. doi: 10.1111/1755-0998.12630. Epub 2016 Nov 21. PMID: 27801980; PMCID: PMC5466693.
  • https://doi.org/10.1111/1755-0998.12630
  • PMID: 27801980
  • PMC: PMC5466693
  • Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.
  • Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN (2016). Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. PLoS Comput Biol 12(3): e1004789.
  • https://doi.org/10.1371/journal.pcbi.1004789
  • PMID: 26938243
  • PMC: PMC4777449
  • Estimating effective population size changes from preferentially sampled genetic sequences.
  • Karcher MD, Carvalho LM, Suchard MA, Dudas G, Minin VN (2020). Estimating effective population size changes from preferentially sampled genetic sequences. PLoS Comput Biol 16(10): e1007774.
  • https://doi.org/10.1371/journal.pcbi.1007774
  • PMID: 33044955
  • PMC: PMC7580988

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