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Tree Fusing

  1. The fuse command implements tree fusing, in which pairs of trees and compared, and all pairs of subtrees that have different resolution but the same terminals are exchanged, in an attempt to find better combinations. We will first run a default fuse ():
                wipe ()
                read ("course.fasta", "swap_course.tree")
                report (treestats)
                fuse ()
                report (treestats)
    
    How many iterations happened?

  2. During an iteration, the program picks two trees at random, a source, and a destination, to compare. When a better tree than the destination is found, fuse replaces it with the better tree.

  3. Note that by default the fuse command does not swap. However, like many other commands in POY, fuse accepts a swap argument. Let's now run a fuse with a swap:
                wipe ()
                read ("course.fasta", "swap_course.tree")
                report (treestats)
                fuse (swap (tbr))
                report (treestats)
    

  4. This time save the trees found for later use:
                report ("fuse_course.tree")
    

  5. Now try to construct a fuse step which lasts for at most 20 seconds. (Use the command documentation section about swap for help.)



Andres Varon, avaron@amnh.org