Abstract

A robust and well-resolved phylogenetic classification is essential to understand genetic relationships within and between species and the evolution of their phenotypic diversity. In the last decade the genomic revolution has represented a drastic change in the amount of data used for phylogenetic inference. The single-gene approach using universal phylogenetic markers for the different lineages across the tree of life, is now being replaced by the assembly of taxon-rich and genome-scale data matrices, the so called phylogenomic approach.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• How do I find a set of common proteins (orthologs) across related species or strains?
• How do I organize a set of orthologs to infer evolutionary relations between species or strains (phylogenetic reconstruction)?

Learning Objectives

• Mask repetitive elements from a genome
• Annotate (predict protein-coding genes) the genomes of the samples to compare
• Find a set of common proteins across the samples (orthologs)
• Align orthologs across samples