I have two questions concerning parsimony phylogenetic analysis in PAUP.
1) When to define outgroups, before or after heuristic searches? I noticed someone stated that do not use the entire out-group as the root, as this forces the putative in-group to form a monophyletic group. I have two outgroup taxa in my dataset, what's the correct practice for me?
2) I had more than 1 trees retained after heuristic search. Which tree should I use to display? Someone said "When multiple MP trees were produced, the tree chosen for display in a figure was the one determined to be most likely using substitution models suggested by ModelTest". But how to know which tree is most compatible with the suggested model?
Any comments are welcome. Thanks.