F Heuristic searches.

When the number of sequences to be evaluated is larger than about 10, it is
necessary to use approximate methods in order to evaluate alternative tree
topologies.  These methods are called heuristic searches.  There are a wide
variety of tree searches and we will use only a few of these.  The usual
approach is to generate a tree (in some fast way) and then swap branches on this
tree, looking for trees with better scores.

The dataset we shall use is a set of primate mitochondrial genes.  This dataset
was collected in order to solve the age-old question concerning the relationship
between humans, chimpanzees and gorillas.  These are the real data used in the
publication in 1988.

1. Take a look at the dataset.  Its format is slightly different, as we are
using a dot "." to indicate that a nucleotide has the same character state as
the first sequence in the dataset (the lemur).  There is also a numbering system
on top of the data matrix that indicates the position in the alignment.

2. Read the dataset into the program's memory.

3. Look at the options for a heuristic search (command 'hs').  The first of the
options concerns the kind of heuristic search that can be carried out.  The
choice is between a "Nearest Neighbor Interchange", a "Sub-tree Pruning and
Regrafting" or a "Tree-bisection and Reconnection" search.  These three kinds of
search are in order of the rigorousness of the approach.

4. Perform a search of trees using the NNI procedure, record the number of trees
searched and the score of the best tree.

5. Use the showtrees command to see the best tree(s).

6. Perform a search of trees using the SPR procedure, record the number of trees
searched and the score of the best tree.

7. Use the showtrees command to see the best tree(s).

8. Perform a search of trees using the TBR procedure, record the number of trees
searched and the score of the best tree.

9. Use the showtrees command to see the best tree(s).

10. Write in your copybook your interpretation of these trees.  What does this
mean for the relationships between these primate species?

11. Use the 'contree' command to generate a consensus tree.  What part of the
tree is 'collapsed' into a trichotomy?  Why?

12. Quit the program.