Pipeline used in: Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences J.L. Leal, Pascal Milesi, Jarkko Salojärvi, and Martin Lascoux Syst. Biol. 72:372–390 (2023) https://doi.org/10.1093/sysbio/syad009 A tutorial is available here.