T-Coffee is distributed under the Gnu Public License
Please make sure you have agreed with the terms of the license attached to the package before using the T-Coffee package or its documentation. T-Coffee is a freeware open source distributed under a GPL license. This means that there are very little restrictions to its use, either in an academic or a non academic environment.
T-Coffee code can be re-used freely
Our philosophy is that code is meant to be re-used, including ours. No permission is needed for the cut and paste of a few functions, although we are always happy to receive pieces of improved code.
T-Coffee can be incorporated in most pipelines: Plug-in/Plug-out…
Our philosophy is to insure that as many methods as possible can be used as plug-ins within T-Coffee. Likewise, we will give as much support as possible to anyone wishing to turn T-Coffee into a plug-in for another method. For more details on how to do this, see the plug-in and the plug-out sections of the Tutorial Manual.
Again, you do not need our permission to either use T-Coffee (or your method as a plug-in/out) but if you let us know, we will insure the stability of T-Coffee within your system through future releases.
The current license only allows for the incorporation of T-Coffee in non-commercial pipelines (i.e. where you do not sell the pipeline, or access to it). If your pipeline is commercial, please get in touch with us.
T-Coffee can be used to automatically check if an updated version is available, however the program will not update automatically, as this can cause endless reproducibility problems.
$$: t_coffee -update