Alignment methods (Part 3: paper discussion)
Previous class check-up
- We studied the algorithms for multiple sequence alignment: Needleman-Wunsch, progresive alignment and improvements
Learning objectives
At the end of today’s session, you will be able to
- highlight the main differences among MSA methods
Pre-class work
Project checklist: heavy HW on your data starting now
- Until now:
- Created your project github repo
- Added the link to the
class-repos.mdvia pull request - Added me as collaborator on your github repo
- Data chosen and added 1 slide about it to the shared google slides (link in canvas)
- Don’t wait on your data: you can use public data because you will be creating scripts to use later on the “real” data
- Added a description about your data in your
notebook-log.md(or similar reproducible script) in your github repo and pushed - QC on your data if needed: not perfect/complete, but at least a plan pushed to your github repo
- Next item:
- Alignment work pushed to your github repo
Expectations as we move forward to heavy HW on your data
- You will be working on your data at home:
- Troubleshooting with different data formats
- Troubleshooting with software installation for your operating system
- Actively ask questions!
- Slack
- Office hours
Alignment software: ClustalW, MUSCLE, T-Coffee
Progressive alignment: ClustalW
- Compute rooted binary tree (guide tree) from pairwise distances
- Build MSA from the bottom (leaves) up (root)
Figure 9.9 in Warnow (2018) Computational phylogenetics
Iterative refinement: MUSCLE
Consistency-based scoring: T-Coffee
In-class paper discussion
Objective: Understand the main algorithms, assumptions and limitations of three widely used MSA software.
Instructions:
- Separate group discussions (25 minutes): Students will discuss with their respective groups and prepare a 10-minute presentation for the whole class. Use these google slides:
-
Group presentations (30 minutes total; 10 minutes per group): Each group will summarize their discussion in a 10-minute presentation to the class.
- Class summary of the three software (10 minutes)