Phylogenetic Inference Using RevBayes

Workshop at NIMBioS - Knoxville, TN USA

August 7-11, 2017

Instructors

• Sebastian Höhna (lead organizer)
• Bastien Boussau
• Emma Goldberg
• Tracy Heath
• John Huelsenbeck
• Will Freyman

Workshop Preparation

To prepare for the workshop, please see detailed information: https://revbayes.github.io/RevBayes-NIMBioS-Workshop/workshop-prep

Workshop Schedule

Detailed schedule timeline: link

Workshop Topics

Repository for slides: https://github.com/revbayes/RevBayes-NIMBioS-Workshop/tree/master/slides

Monday, 7 August - Höhna & Hülsenbeck

Topics

• Introduction/Overview
• Probability, Bayesian Statistics, MCMC
• Likelihood based phylogenetics [slides]
• Introduction to RevBayes [slides]

Practical: Introduction to RevBayes

• Tutorial PDF: RB_MCMC_Intro_Tutorial.pdf

Practical: Models of Molecular Evolution

• Tutorial PDF: RB_CTMC_Tutorial.pdf
• Primates data
• JC Rev script
• GTR+I+G Rev script

Tuesday, 8 August - Höhna, Hülsenbeck, & Freyman

Topics

• Partition Models and Model Selection [slides]
• Model Fit [slides]
• MCMC Diagnostics & Convergence

Practical: Model Selection

• Tutorial PDF: RB_BayesFactor_Tutorial.pdf
• Data file
• Rev script

Practical: Partition Models

• Tutorial PDF: RB_Partition_Tutorial.pdf
• Data files
• Rev scripts

Practical: Model Fit

• Tutorial PDF: RB_PosteriorPrediction_Tutorial.pdf
• Data files
• Rev scripts

Practical: MCMC & Convergence

• Tutorial PDF: RB_MCMC_Tutorial.pdf
• Rev scripts

Wednesday, 9 August - Höhna & Heath

Topics

• Divergence-time estimation [slides]
  • Clock Models
  • Node Calibration
  • Total Evidence Analysis

Practical: Clock Models

• Tutorial PDF: RB_ClockModels_Tutorial.pdf
• Data file
• Tree file
• Rev scripts

Practical: Total Evidence Analysis under the Fossilized Birth-Death Process

• Tutorial PDF: RB_TotalEvidenceDating_FBD_Tutorial.pdf
• Data files
• Rev scripts

Thursday, 10 August - Höhna, Goldberg, & Freyman

Topics

• Estimating Diversification Rates Through-Time
• Lineage-Specific Diversification Rates
• Character State-Dependent Diversification Rates
• Biogeography
• [slides for second two topics]

Practical: Basic diversification using constant-rate birth-death models

• Tutorial PDF: RB_DiversificationRate_Tutorial.pdf
• Data files
• Rev scripts

Practical: Diversification rates through time using episodic birth-death models

• Tutorial PDF: RB_DiversificationRate_Episodic_Tutorial.pdf
• Data files
• Rev scripts

Practical: Branch-specific diversification rate estimation

• Tutorial PDF: RB_DiversificationRate_BranchSpecific_Tutorial.pdf
• Data files
• Rev scripts

Practical: Character state-dependent diversification

• Tutorial PDF: RB_DiversificationRate_CharacterDependent_Tutorial.pdf
• Data files
• Rev scripts
• RevGadgets R package

Practical: Biogeography

• Tutorial PDF: RB_Biogeography_Tutorial.pdf
• Data files
• Rev scripts
• Also, the second part of the Biogeography Practical uses the Character state-dependent diversification materials above.

Friday, 11 August - Höhna & Boussau

Topics

• Gene-tree/species-tree estimation
• The multispecies coalescent model

• [slides]

• Tutorial PDF: RB_MultispeciesCoalescent_Tutorial.pdf
• Data files
• Rev scripts
• Starting gene trees
• Example outputs of the MCMC, basic MSC
• Example outputs of the MCMC, MSC with conjugate prior