4 Visualizing data before use
A key step in any analysis is looking at the data. If you have loaded protein coding DNA sequences, are they aligned correctly? Are the codon positions specified correctly? For trait data, is everything measured in the same units, or are some oddly a thousand-fold higher than others? Are you dealing with an older dataset format that uses -1 or 19 for missing data, and have you incorrectly treated those as observations? Is your tree ultrametric?
It is easy to overlook this step, but you can draw the wrong conclusions based on errors at this stage. Most peer reviewers will not notice this, either, so your error could slip into the literature and mislead others. Take the time to get to know your data.