Abstract
Phylogenetic analysis has become a common step in characterization of gene and protein sequences. However, despite the availability of numerous affordable and more-or-less intuitive software tools, construction of biologically relevant, informative phylogenetic trees remains a process involving several critical steps that are inherently non-algorithmic, i.e., dependent on decisions made by the user.
These steps involve, but are not limited to, setting the aims of the phylogenetic study, choosing sequences to be analyzed, and selecting methods employed in sequence alignment construction, as well as algorithms and parameters used to construct the actual phylogenetic tree. This review aims towards providing guidance for these decisions, as well as illustrating common pitfalls and problems occurring during phylogenetic analysis of plant gene sequences.