Ancestral Sequence Reconstruction from Multiple Sequence Alignment using Mesquite

Question

[anuragm]

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.

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?

Answer 1

[rmccloskey]

As far as I know, Mesquite has support only to reconstruct a single discrete state at a time. So if you want to reconstruct the entire ancestral sequence, you would have to encode each position as a separate state (like the categorical example data), then reconstruct them all separately. Obviously this is quite a hassle, so you might try using a different tool. In the past I've used HyPhy to do ancestral sequence reconstruction: there is a code example here but documentation is fairly scarce. Alternatively, FastML can do ancestral state reconstruction.