Graduate Phylogenetics - Spring 2024

University of California, Merced – QSB/ES 244

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

Instructor: Emily Jane McTavish

Time/Location: Lecture/Lab, Wednesday 9 AM - 12 PM, Granite Pass 115

Web View: https://mctavishlab.github.io/GradPhylo

Please complete setup instructions listed at https://mctavishlab.github.io/GradPhylo/installs

New materials will be posted here, material from when this was taught in 2022 at https://mctavishlab.github.io/GradPhylo/gp2017

Jan 17, 2024
Class intro
Tree thinking quiz 1
Tree thinking quiz 2
Tree formats and terms

Jan 24, 2024 Using the UC Merced HPC Intro to computation

Jan 31, 2024 Phylo thinking
Discussion: Covid + Phylogenetic applications
Lab: NextStrain

Feb 7, 2024
Phylogenetic inference_and_likelihood_intro
Lab: iqtree lab

Feb 14, 2024
More likelihood
Super cool widgets developed by Mark Holder:
Barcharts
Branch length
Optimization

Feb 21, 2024
Models
Dire Wolf discussion paper
Maximum likelihood tree search
Lab: ML search

March 13, 2024
Paper discussions

March 20, 2024
Bayes Intro + Monte Hall Paper discussion:

April 3, 2022
More Bayes - exercises from Paul Lewis
MCMC Robot
MCMC example

April 10, 2024
MrBayes lab from Paul Lewis

April 17, 2024
Data choices
Paper: Phylogenetic tree building in the genomic age
Paper: Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences

April 24, 2024
Open Tree of Life
OpenTree Demo link
Comparative analysis guest presentation - Ronnie Hall
Comparative anaysis text - Luke Harmon
Suggested comparative analysis tutorials from Ricardo Betancur, Luke Harmon, & Liam Revell
Paper:

May 1, 2024 Divergence time estimation Gene Tree Species Trees

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