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T-Coffee & Co

Installing T-Cofee, ClustalW and SAP

1. Download and install CLUSTALW


  • Example:

    tar xvfz clustalw1.83.linux.tar.gz
    cd clustalw1.83.linux
    cp makefile.linux makefile
    cd ..
    sudo mv clustalw1.83.linux /usr/local/src/clustalw1.83
    sudo ln -s /usr/local/src/clustalw1.83/clustalw /usr/local/bin/

    There may be a more elegant way. I just didn't find it yet. Clustalw is also available as Ubuntu package clustalw.

2. Download and install SAP

  1. download and unpack and compile the non-official SAP distribution, for example:

    tar zxvf sap_repackaged
    cd sap_distribution/source
    make sap
  2. link or copy sap into your path, for example:

    sudo cp ../bin/sap /usr/local/bin


    The source code for SAP is "freely available for non-profit academic work" from Willie Taylor's ftp folder: and

    Cederic Notredame kindly sent us is own re-packaged version for easier compilation.

3. Download and install T-COFFEE


    For example(please adapt the download link):

    tar zxvf T-COFFEE_distribution*.tar.gz
    rm T-COFFEE_distribution*.tar.gz
    sudo mv T-COFFEE_distribution_Version* /usr/local/src
    cd /usr/local/src/T-COFFEE_distribution_Version*
    sudo ./install t_coffee
    cd /usr/local/bin
    sudo ln -s ../src/T-COFFEE_distribution_Version*/bin/binaries/linux/t_coffee .

    Ensure that all folders in the newly created ~/.t_coffee belong to your user (replace raik:users by your own login and group name):

    sudo chown -R raik:users .t_coffee


    An outdated version of T-Coffee is also available as Ubuntu package t-coffee

4. Configure Biskit & T-Coffee

  1. option 1: via the biskit exe_t_coffee.dat config file:

    • make a local copy of the Biskit Executor configuration for T-Coffee:

      cp biskit/Biskit/data/defaults/exe_t_coffee.dat ~/.biskit/
    • adapt the parameters:

      bin = /path/to/t_coffee  ## if not in $PATH
      CLUSTALW_4_TCOFFEE = /path/to/clustalw
      SAP_4_TCOFFEE = /path/to/sap
      ... # more env. variables are optional (see below)
  2. option 2: via normal environment variables (works also w/o biskit)

    • make sure t_coffee is in your $PATH
    • setenv CLUSTALW_4_TCOFFEE /path/to/clustalw
    • setenv SAP_4_TCOFFEE /path/to/sap
  3. Optional settings

    • force T-Coffee not to validate filenames of structures against the RCSB. The validation is quite time consuming, therefore this setting is recommended. setenv NO_REMOTE_PDB_DIR 1
    • If you have a local database installed this can be used for the validation. setenv PDB_DIR /path/to/your/pdb/database

5. Test T-Coffee / SAP / ClustalW

  • Execute the Biskit unittest:

    cd biskit/Biskit/Mod
  • This should (after some time and a lot of other output) result in something like this:

    The alignment result is in /tmp/tmp1SewRJ_test_Aligner/t_coffee
    Ran 2 tests in 99.918s


    The test result is by default deleted. In order to prevent this, you can change the last line in (works for any other Biskit module) to:


    Problems? See also: T-Coffee troubleshooting!

  • see Biskit.Mod.Aligner
  • see scripts/Mod/
Custom configuration:
see biskit/external/defaults/exe_t_coffee.dat