How to install “tr2”

Once the environment is properly set up, the installation of tr2-delimitation is fairly simple. Download the file of tr2-delimitation from the bitbucket repository and decompress it in any place in your computer.

Just click a cloud-like icon on the left side pane and then click “Download repository” to start downloading. A decompressed folder may have a long name  like “tfujisawa-tr2-delimitation-84f248b5fa48”. Simply rename it like “tr2” if you want a handy access to the folder.

To test if the tr2 (and the environment) is correctly installed, let’s run it with a test data set.

$cd /path/to/yourfolder/tr2-delimitation #move to the installed folder
$python run_tr2.py -t sim4sp/simulated.gene.trees.nex10.4sp.tre -g sim4sp/guide.tree.4sp.tre

If you see a table of delimitation like below, the installation is successful.

write: <stdout>

species sample
1 1.1
1 2.1
1 3.1
1 4.1

...

4 17.4
4 18.4
4 19.4
4 20.4

 

In Unix-like OS’s, the program can be run without calling with python.

$./run_tr2.py -t sim4sp/simulated.gene.trees.nex10.4sp.tre -g sim4sp/guide.tree.4sp.tre

 

If you installed python with Anaconda and created a python2 environment, you need to first activate it,

$activate python2
$python run_tr2.py -t sim4sp/simulated.gene.trees.nex10.4sp.tre -g sim4sp/guide.tree.4sp.tre

 

You can integrate delimitation with species tree inference using the rooted triple consensus. To set up the triplec program, download it from its website, and create a folder named “bin” in the same folder as run_tr2.py and put the triplec in the “bin” folder.

$python run_tr2.py -t sim4sp/simulated.gene.trees.nex10.4sp.tre

If the command above returns a similar outputs, the triplec is correctly called.

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