B Trees

README for Comparative genomics practical.


            Shape of trees and tree topologies.

Aim: This practical session reviews the concepts of trees and tree topologies. 

You will use the program 'retree' from the PHYLIP packages of programs. The
PHYLIP package was one of the first package of programs for performing
phylogeny reconstruction.  The package was written by Dr. Joe Felsenstein in
Seattle, Washington.

Retree can be used to read a file containing the 'nested parentheses'
description of a tree.
The following is an example of a nested parenthesis tree file:

    (Cow,((Mouse,Rat),(Chimp,Human)));

This tree indicates that the human and chimp are each others closest relatives,
the Mouse and Rat are each others closest relatives and the Cow is not
specifically related to any of the terminal taxa.

Task 1: Read the treefile into memory.

1.  Start the program retree by typing its name:

        linux$ retree
        
2.  You should see a screen that looks something like this:


--------------------------------------------------------------------------------
Tree Rearrangement, version 3.6a2.1

Settings for this run:
  U          Initial tree (arbitrary, user, specify)?  User tree from tree file
  N   Format to write out trees (PHYLIP, Nexus, XML)?  PHYLIP
  0                     Graphics type (IBM PC, ANSI)?  (none)
  W       Width of terminal screen, of plotting area?  80, 80
  L                        Number of lines on screen?  24

Are these settings correct? (type Y or the letter for one to change)
--------------------------------------------------------------------------------


3.  We shall accept all the default options.  You can do this by typing the
letter 'y'.  If you wanted to change any of the options, you could do so by
typing the character that appears in the leftmost column (L,N,0,W,L).

4. The program now asks you for the name of the tree file.  We have placed a
treefile in this directory.  Its name is Mammal.tre and it contains the tree
detailed above.  You should now be seeing the following:

--------------------------------------------------------------------------------
Reading tree file ...

retree: can't find input tree file "intree"
Please enter a new file name> 
--------------------------------------------------------------------------------

Enter the name of the treefile (Mammal.tre)

5. You should now see an ASCII-character tree and a series of options like this:


--------------------------------------------------------------------------------
  ,>>>>>>>>>>>1:Cow
  !  
--6        ,>>2:Mouse
  !  ,>>>>>8  
  !  !     `>>3:Rat
  `>>7  
     !     ,>>4:Chimp
     `>>>>>9  
           `>>5:Human


NEXT? (Options: R . U W O T F D B N H J K L C + ? X Q) (? for Help) 
--------------------------------------------------------------------------------

6.  The program has read the nested parentheses file and has represented this
tree on the screen.  You can see from this treefile that the Chimp and Human are
joined to each other through a single node (node number 9).  Can you describe
the rest of the tree and the nodes that join various groups?

7. In order to see the options that are available to us, you can type the
question mark.  You should then see the following:

--------------------------------------------------------------------------------
 . Redisplay the same tree again
 U Undo the most recent change in the tree
 W Write tree to a file
 + Read next tree from file (may blow up if none is there)

 R Rearrange a tree by moving a node or group
 O select an Outgroup for the tree
 T Transpose immediate branches at a node
 F Flip (rotate) subtree at a node
 D Delete or restore nodes
 B Change or specify the length of a branch
 N Change or specify the name(s) of tip(s)

 H Move viewing window to the left
 J Move viewing window downward
 K Move viewing window upward
 L Move viewing window to the right
 C show only one Clade (subtree) (might be useful if tree is too big)
 ? Help (this screen)
 Q (Quit) Exit from program
 X Exit from program

 TO CONTINUE, PRESS ON THE Return OR Enter KEY
--------------------------------------------------------------------------------

 
 8. Type 'F' and flip the branches at node 7.  Draw the resulting tree and
comment on whether or not it has the same meaning as the original tree.

9.  Type 'F' again and this time flip node 8.  Draw the tree again and once
again comment on what it now means.

10. Specify the mouse as the outgroup of the tree.  How does this affect the
tree?  Does it make sense?

11. Experiment with options R, T, D, C and N.

12. Quit when you are finished.


