How is tree building an art?
Tree building is kind of an art. There are many different options for every step in making a tree (phylogeny. fr is great because it describes these options and allows you to swap between them). This variability stems from the problem that making a perfect tree by trying all the options is computationally impossible. All programs must reduce the problem to being feasible, requiring assumptions and choices to be made. Each one makes different assumptions in its algorithms, and each performs well in different situations.
What is phylogenetic analysis using maximum likelihood?
Phylogenetic Analysis Using Maximum Likelihood PAML is a program that intakes PHYLIP 4.0 format which can include tree data. This program can be used to make trees, but it’s older and clunkier, but it does allow for the analysis of selection parameters, omega, etc. Here is a good overview/tutorial.
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