UC Merced QSB/ES 244

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Graduate Phylogenetics -Spring 2020

University of California, Merced – QSB/ES 244

A graduate course covering phylogenetic methods: theory, statistics and practice.

Instructor: Emily Jane McTavish

Time/Location: Lecture/Lab, Wednesday 1:30 - 4:30, SSM 150 (optional lab time 4:30-5:30)

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Please complete setup instructions listed at

New materials will be posted here, material from when this was taught in 2017 at

Complete tree thinking quiz before first class
Intro slides
Week 1 slides Tree terminology and applications
Week 2 slides Inferring trees from data
Intro to HPC slides Intro to computation
Likelihood 1 Intro to likelihood
Maximum likelihood tree search ML tree search
ML search lab ML search lab
Models Models
IQTree beginner tutorial IQtree tutorial
Bayesian inference intro Bayesian inference intro
Bayesian inference II Bayesian inference 2
MCMC assignment from Paul Lewis MCMC assignment
MrBayesLab Mr Bayes tutorial
Dating Trees Dating Trees
OPTIONAL Computer lab on BEAST 2: introduction
OPTIONAL Computer lab on BEAST 2: divergence time estimation Reproducibility Guest Lecture by Luna Luisa Sanchez Reyes
Genomic Phylogenetics
Gene Tree Spp Tree
Handling discordance

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