General information and course material
General objectives
Interpret phylogenetic trees and alignments; general understanding of how trees are inferred; knowing the definition of orthology, paralogy and their subtypes; understanding the difference between pairwise and groupwise comparisons; ability to perform orthology inference through tree overlap method; ability to retrieve orthology information from the OMA database; ability to infer orthologs using the OMA standalone pipeline.
Course material
Lecture: Overview, objectives, motivation, concept of orthologs, HOGs
Module 1: Genes, groups, and genomes in the OMA Browser
Module 2: Fast placement with OMAmer
Module 3: FastOMA
Module 4: Building Species Trees
Course gitlab repository
The gitlab repository to run all the practicals is available at https://github.com/DessimozLab/SIBBiodiversityBioinformatics2023.
Note
Remember to open a Gitpod workspace before starting the practicals. Click here for more information on Gitpod workspace.
Working directories
You can find the working directories of Modules 2, 3, and 4 in the following list:
Exercises ouputs
You can find the expected outputs of Modules 2, 3, and 4 in the following list: