MegaTree is a workflow that creates a Mutiple Sequence Aligment (MSA) of amino sequences using Clustal Omega [1], computes an evolutionary tree with IQ-TREE 2 [2] and finally visualizes the tree and MSA using R/ggtree.
[1] Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear, IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era, Molecular Biology and Evolution, Volume 37, Issue 5, May 2020, Pages 1530–1534, https://doi.org/10.1093/molbev/msaa015
[2] Sievers, Fabian, Wilm, Andreas, Dineen, David, Gibson, Toby J, Karplus, Kevin, Li, Weizhong, Lopez, Rodrigo, McWilliam, Hamish, Remmert, Michael, Söding, Johannes, Thompson, Julie D, Higgins, Desmond G, (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7. 539. doi: accession:10.1038/msb.2011.75