Further reading#

Phylogenetic tree thinking: Interpreting phylogenetic trees seems a priori a simple task, since it is indeed a simple representation of a dichotomic diversification. Yet as we have seen throughout this crash course, a phylogenetic tree might lead to misinterpretation when not interpreted from an integrative methodological and biological perspective (Meisel 2010). In this context, a single tree provides one version of a very complex process that requires a critical thinking and interpretation from many different points of view (Doolitle and Bapteste, 2007).

Regarding the methodological aspect of phylogenetic reconstruction, models and parameters you can directly check in the (most of the times) very well documented hands-on tutorials of the open source softwares I introduced here. Besides, I highly encourage you to extend your possibilities and go fancy in phylogenetic inference by looking and exploring different options through the help command (i.e.; iqtree -h, raxml-ng -h), or through their online manuals and hands-on tutorials: