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tutorials:eccb_t2_tdg09 [2012/09/06 16:30] romainstuder created |
tutorials:eccb_t2_tdg09 [2012/09/08 16:26] (current) romainstuder |
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| + | ==== 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> | <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)): | 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> | <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. | The output is put in the file tdg.out. | ||
| - | We need to transform it with some unix tools: | + | 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> | <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 | + | 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> | </code> | ||
| Line 32: | Line 60: | ||
| </code> | </code> | ||
| - | == Jalview | + | == Jalview == |
| Load multiple alignment: H1.faa | Load multiple alignment: H1.faa | ||
| (you will need to remove the first line, as it is in Phylip format. | (you will need to remove the first line, as it is in Phylip format. | ||
| Line 40: | Line 68: | ||
| Put a vertical line a the root of the tree to split the tree in two. | Put a vertical line a the root of the tree to split the tree in two. | ||
| - | => Visualise the position of these sites | + | => Visualise the position of these sites. |
