Additional resources for constructing phylogenetic trees

Users can perform sequence alignment through the MAFFT website (Katoh and Standley, 2013; Katoh et al., 2019 ) and then build phylogenetic trees through IQ-TREE (Nguyen et al., 2015) to further determine and characterize homologous genes/proteins related to plant stem cells. In addition, users can modify phylogenetic trees through ITOL (Letunic and Bork, 2021).

References

Katoh, K., Rozewicki, J., and Yamada, K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20:1160-1166.
Katoh, K., and Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772-780.
Letunic, I., and Bork, P. (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49:W293-W296.
Nguyen, L.H., Schmidt, H.A., von Haeseler, A., and Minh, B.Q. (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 35:268-274.