This is a complete tutorial for the workshop "Phylogenetic Network reconstructions" by Kevin I. Sanchez and Melisa Olave (Sept. 2023).
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
Also note that there are very good tutorials available on PhyloNetworks website