Combining morphological and DNA sequence data for phylogenetic analysis

I'm an evolutionary biologist based in the Department of Zoology, University of Cambridge (www.robertjasher.com). Here I describe very basic steps to join phylogenetic data typical in paleontology (morphological characters) with DNA sequences from living species in order to make a phylogenetic estimate of fossils in the context of their living relatives. In this exercise I use nexus format and draw mostly from these data sources and software packages: Huttenlocker et al. 2018: https://www.nature.com/articles/s41586-018-0126-y Upham et al. 2019: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892540/ Asher 2007: http://www.biomedcentral.com/1471-2148/7/108/abstract and http://www.robertjasher.com/database/morphsite_bmc07.html PAUP by David Swofford: http://paup.phylosolutions.com/ Notepad++: https://notepad-plus-plus.org/ The starting image is a beautiful rendering of two Triassic fossils from South Africa, a cynodont related to modern mammals (Thrinaxodon) and a temnospondyl related to modern amphibians (Broomistega). Credit for this image (https://upload.wikimedia.org/wikipedia/commons/5/52/Odd_couple.png) goes to Fernandez V, Abdala F, Carlson K, Cook D, Rubidge B, Yates A, Tafforeau P (2013). "Synchrotron Reveals Early Triassic Odd Couple: Injured Amphibian and Aestivating Therapsid Share Burrow". PLOS ONE. DOI:10.1371/journal.pone.0064978.