This is a complete tutorial for the workshop "Phylogenetic Network reconstructions" by Kevin I. Sanchez and Melisa Olave (Sept. 2023).

Organization

01_genetrees.md: tutorial for gene tree estimation in raxml

02_sptree.md: tutorial for species tree inferences using ASTRAL (using gene trees) and SVDQuartets (using SNPs)

03_network.md: tutorial for phylogenetic network estimation using PhyloNetworks (gene trees and SNPs)

04_trait_on_Networks.md: tutorial to test transgressive evolution of traits on networks and ancestral states reconstructions

External links

Also note that there are very good tutorials available on PhyloNetworks website