TOPIC: Population Genetics and Comparative Genomics

A repository for the lessons and tutorials for the Population Genetics and Comparative Genomics TOPIC channel of the BVCN

Prerequisites

• A working Unix environment
• Experience with the command line

Overview

This BVCN topic will cover:

• An overview of transcriptomics and metatranscriptomics
• Lessons covering various applications, including:
  • Wetlab and in silico rRNA depletion
  • Recovery/removal of rRNA from metatranscriptomic data

Lessons

Lesson 1 -- Comparative Genomics using dN/dS, with PAML (Codeml)

Instructors: Arkadiy Garber and Jake Weissman

• Synonymous vs. nonsynonymous mutations:
  • Estimating selection using dN/dS
  • Limitations of dN/dS
• Introduction to PAML
  • PAML programs
  • Input and output files
  • Making a codon alignment
  • The codeml.ctl file
  • Running codeml

Watch the lesson

Follow the tutorial

Lesson 2 -- An Extremely Brief Introduction to the McDonald-Kreitman Test for Selection

Instructors: Jake Weissman and Arkadiy Garber

• Why the MK-Test?
• Intuition behind the test
• Running the test on a large set of genes from Listeria monocytogenes

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Lecture Slides

Follow the tutorial

Lesson 3 -- Phylogenetically Structured Data (aka The Statistical Dangers of Between-Species Comparisons)

Instructors: Jake Weissman and Ben Tully

• Between-species comparative studies
• Dealing with phylogenetic structure (detecting phylogenetic signal in traits, correcting for it with PGLS)

Watch the lesson

Lecture Slides

Follow the tutorial