Software

Polytree:

• You can access the polytree software on the web at www.dina.dk/~sestoft/bsa/Match7Applet.html, or
• you run it locally it as
  java -jar /users/students4/software/public/Bio4/bin/PolyTreeToy.jar
  under linux. Note that polytree does not implement neighbour-joining correctly -- the trees are displayed as rooted!.

Phylip:

• You can access Phylip as a web-service at http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
• You can run Phylip by typing the name of one of the modules
  e.g. neighbor. Be careful to run these programs from your own directory since they will need to write out files as they run! You do not need to give any arguments to the programs - they will put up a [basic] dialogue for you to interact with.
  A list of programs in the phylip package is at http://evolution.genetics.washington.edu/phylip/programs.html
• If you are really keen, after the lab, you can download and install Phylip from http://evolution.gs.washington.edu/phylip

Blast:

• Blast is installed at /usr/local/lab/packages/blast-2.2.14/bin/, e.g.
  you can run it by typing, blastall

Exercises

(A) Identify the phylogeny of Globin Sequences (Beta-Chain).

Using Clustalw/Phylip to compute distances/matrices: step by step.

1. Download the globin sequences (amino-acids, in fasta format) from the course website
2. Use clustalw as either the command-line version or the web-based version (see Lab 4).
   E.g. (web-based):
   • Open the page for clustalw. Upload the file with the help of the "Browse..."-button.
   • Use the default settings and make sure that the output format PHYLIP is selected. (The produced format, the PHYLIP format is needed in the next step).
   • Click on "Submit" and run the sequence alignment.
   • Copy the alignment into a new text file and save it. (this will be the input file for the PHYLIP programs). E.g. 'globins_all.phy'
3. Go to the directory where that you have saved the input file.
4. Calculate the distance matrix for the input file. In your terminal, invoke the protdist program by typing the command
   protdist
5. Enter the input file name (of your alignments from clustalw) to the console. E.g. 'globins_all.phy'
6. protdist outputs an outfile that calculates the distance matrix.
7. Change the name for this outfile (e.g. mv outfile outfile.matrix)
8. Now we will produce neighbour-joining trees for the input sequences using neighbor. Invoke the neighbor program by typing the command
   neighbor
9. Enter the matrix file name to the console. (e.g. outfile.matrix)
10. You can choose to produce a Neighbour-joining tree or a UPGMA tree from the console.
11. neighbor outputs two different files, the outfile (tree visualisation) and the treefile (distances).
12. You can plot an unrooted tree (for neighbour-joining) using
    drawtree
    or a rooted tree (for UPGMA) using
    drawgram
    which will require your treefile
    Note that this program will also ask you for a 'fontfile'; these are
    /users/students4/software/public/Bio4/bin/phylip3.65/font1
    /users/students4/software/public/Bio4/bin/phylip3.65/font2
    up to font6
13. You can try to generate trees using the fitch or kitsch programs from the phylip package. You can plot these using either the drawtree or drawgram programs.

(B) Origin and evolution of HIV