Compatibility

A main tenet in this course is compatibility. Does your output really work with other established software? This will be explored here.

Compute the evolutionary tree

Use your program from the previous assignment to compute distances for the chosen species. Then run Phylip's program neighbor to estimate the phylogenetic tree.

On Ubuntu computers, you start neighbor with the command

   phylip neighbor

and the program then expects to find the input in a file called "infile". You are however offered to suggest another file if "infile" does not exist.

Where does the output go?

To present:

1. What does the program neighbor do? You only need to explain what it tries to compute, not how it does it.
2. Show that the output of your program is indeed compatible with neighbor.
3. What can you say about the output?