==== TDG09 ====

=== Installation ===

Download from here:
[[http://www.homepages.ucl.ac.uk/~ucbtaut/]]

[[http://bit.ly/fVbnDr]] => tdg09.zip
<code>
unzip tdg09.zip
</code>

=== Detection of site in the Influenza Virus Hemagglutinin HA1 chain ===

We would like to know which sites are important between the Hemagglutinin HA1 of the virus in Avian (genes starting with Av_) and in Human (genes starting with Hu_).

<code>cd ./Tutorial/tdg09  # Folder of installation</code>

The execution of TDG09 with this dataset could take 20 minute or more, depending of the computation power.

Lauch TDG09 with this command (it takes time (20 minutes or more)):

With Linux or MacOSX, you can run the command like this:
<code>./run.sh etc/H1.faa etc/H1.tree > tdg.out</code>

With Windows, you need to execute the whole command:
<code>
java -cp lib\commons-lang-2.4.jar;lib\flanagan.jar;lib\pal-1.5.1.jar;dist\tdg09.jar models.MainAvHu09 etc\H1.faa etc\H1.tree
</code>

The output is put in the file tdg.out.
We need to transform it with some unix tools (the four lines are one unique command):
(/!\ These Unix tools need Cygwin to work in Windows /!\ If you don't have Cygwin, you can continue the tutorial by skip the R part. The sites are given at the end).

<code>
grep "Site\|Parameters\|Log\-likelihood" tdg.out \
| tr '\n' ' ' | sed "s/Site: /\\`echo -e '\n\r'`/g" \
| awk '{$1=$1}1' OFS=" " \
| cut -d' ' -f1,4,7,10,13 > tdg2.out
</code>

Now, we need to load this file tdg2.out into R

# Launch R
<code>
R
</code>

And put these commands:
<code>
tdg.out <- read.csv('tdg2.out', sep=' ', header=F)                                               # Load file
tdg.out <- tdg.out[!is.na(tdg.out$V2),]                                                          # Remove conserved sites
tdg.out$lrt <- pchisq(2 * (tdg.out$V5 - tdg.out$V3), df=(tdg.out$V4 - tdg.out$V2), lower.tail=F) # Perform likelihood test
tdg.out$fdr <- tdg.out$lrt * length(tdg.out$lrt) / rank(tdg.out$lrt)                             # Get false discovery rate (FDR)
tdg.out[tdg.out$fdr < 0.20, "V1"]             # Print all sites under FDR=20% (very relaxed)
tdg.out[tdg.out$fdr < 0.05, "V1"]             # Print all sites under FDR=5% (medium) 
tdg.out[tdg.out$fdr < 0.01, "V1"]             # Print all sites under FDR=1% (stringent) 
 [1]   2   9  62 130 155 168 169 173 177 202 203 204 212 239 252 253 275 276 286
[20] 289 300 303 315 325 416 421 460 471
</code>

== Jalview ==
Load multiple alignment: H1.faa
(you will need to remove the first line, as it is in Phylip format.
=> Sort by ID.

Load tree: H1.tree
Put a vertical line a the root of the tree to split the tree in two.

=> Visualise the position of these sites.