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Day 7: Pangenome trees

Pangenome Trees

In this exercise we will compute pan-genome trees. This is a gene-content tree that illustrates similarities/differences between genomes inside a pan-genome.

The following is a condenced version of a guide that Lars has written for you. Keep this guide on the screen with you, because that one also contains the whys and the wherefores of what you are doing.

# log in to the computers again as, then:
ssh -Y ibiology
umask 022
setenv MAKEFILES /home/people/pfh/bin/Makefile

Create directory for this exercise

# create directory 
mkdir panTree
cd panTree

Copy Buchnera pangenome family tree into your dircetory and unpack it

# copy the file containing the data you will need into your directory 
cp /home/people/larssn/pantree/pantree.tar.gz .
gunzip pantree.tar.gz
tar xvf pantree.tar

Go into the blast directory and start R
```
# log in to the computers again as, then:
cd pantree/buchnera/blast
R-2.8
```
Once you have started R, you will see that the promt, the characters at the beginning of the lines change. This means that you are inside the program R. To exit this program, type q() and answer yes.

Run the script which will prepare the fasta files

# run the script that prepares tha fasta files
source( “script_fastaprep.R” )

Run the script that will compare all proteins with all of the other proteins

In this case the organisms that we are comparing are fairly small, so this will take little time.
```
# run the script that does the blasting, and then quit R
source( “script_blastall.R” )
q()
```
Restart R in a new directory

IMPORTANT: you have to quit R above, before changing directory, otherwise the next part will not work
```
# move to a different directory and start R again
cd ..
R-2.8
```

Prepare gene families

# run the script that creates gene families
source( “script_panMatrix.R” )

Create pan gene family tree plot
```
# create tree
source( “script_panTree.R” )
```
You should now have a plot on your screen.

Save plot

# save as postscript file
dev.copy(device = postscript, file = "pangenomeplot.ps")

Quit R
```
# quit R
q()
```

Exercises created by Karin Lagesen, Lars-Gustav Snipen and Peter F. Hallin