I have a nexus tree file and a multiple sequence alignment(MSA) in nexus format. I am interested in ancestral sequence reconstruction using Mesquite. I had been following this tutorial : http://phylo.bio.ku.edu/slides/lab9-MesquiteAncStatesBisse/09-Mesquite.html#Part_B:_Estimating_ancestral_states
But after the step that says convert the tree display to 'balls and sticks' and Branches proportional to lengths, I am not seeing a Ancestral Reconstruction option when I click the Analysis tab in the trees window.
A difference is that my data is a sequence alignment whereas the data in the example on the webpage is categorical. What is it that I am doing wrong ? Is there a way to do it with a MSA ?