Parallel T-Coffee (PTC) is the first parallel implementation of the TCoffee multiple sequence alignment tool. It has been developed to overcome main limitations of the original method. It is based on the MPI and RMA mechanisms, and it can be run on distributed memory clusters. PTC supports a majority of options provided by TCoffee 3.79, including the 3D-Coffee mode. It can be used to align data sets consisting of hundreds of proteins in reasonable time limits. Parallel T-Coffee is (or has been) developed by Jaroslaw Zola, Xiao Yang, Adrian Rospondek and Srinivas Aluru.
In addition to run 3D-coffee mode
The latest version of Parallel T-Coffee is 1.914 released on 29 Aug 2012. Parallel T-Coffee is distributed under GNU General Public License version 2, mpiext component is distributed under Boost Software License version 1.0.
The bundle provides a comprehensive documentation explaining how to install and use PTC. If you find this software useful and you would like to share your experience with us, or you would like to see some additional features in it, please send a feedback to Jaroslaw Zola.
Three example data sets aligned by PTC. Please note that the sequential program was not able to align them on Xeon 3GHz with 2GB of RAM.
When using Parallel T-Coffee please cite:
J. Zola, X. Yang, S. Rospondek, S. Aluru: Parallel T-Coffee: A Parallel Multiple Sequence Aligner, In Proc. of ISCA PDCS-2007, pp. 248-253, 2007.