Dear Promateus,

This is a very simple thing to do in HyPhy!  We refer to this exercise as fitting a "local" evolutionary model.  Here's a walkthrough on how to go about obtaining estimates for each node (i.e. branch) in the tree.

1. Open your alignment in the HyPhy GUI by selecting the menu option File > Open > Open Data File..., and locating your file in the browser window that appears.

2. Select the entire alignment by selecting the menu option Edit > Select All.

3. Convert your selection into a 'data partition' by selecting Data > 'Selection -> Partition'

4. A new row will appear in your partition list below your alignment in the data viewer window.  Select the option "Codon" under the column Partition Type, specifying offset and genetic code in the window that appears.

5.  Under the column "Tree", select the tree topology either by choosing a file with a Newick string, loading one from memory, or estimating a tree de novo.

6. Under the column "Model", select a model of codon evolution, e.g. MG94xHKY85_3x4.

7. Under the column "Parameters", the option should read "Local".

8. Generate a likelihood function from these settings using the menu option Likelihood > Build Function.

9. Optimize the LF by selecting the menu option Likelihood > Optimize.

10. After HyPhy has obtained maximum likelihood estimates, a window should appear displaying the parameters of the likelihood function.  Each node has a unique identifier that is either the sequence name or "Node #".  Because you've fit a local model, each node is associated with a dN and dS parameter estimate.