Add deprecation warning

docs/index.rst

@@ -6,6 +6,12 @@
 pVAC-Seq
 ====================================
 
+.. warning::
+    pVAC-Seq has been renamed to pVACseq and is now part of the pVACtools
+    immunotherapy tools suite. The ``pvacseq`` package will no longer be
+    updated or maintained. Please update your local installation to the ``pvactools``
+    package. Please see the `pVACtools documentation <http://pvactools.readthedocs.io/>`_ for more information.
+
 pVAC-Seq is a cancer immunotherapy pipeline for the identification of **p**\ ersonalized **V**\ ariant **A**\ ntigens by **C**\ ancer **Seq**\ uencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). It enables cancer immunotherapy research by using massively parallel sequence data to predicting tumor-specific mutant peptides (neoantigens) that can elicit anti-tumor T cell immunity. It is being used in studies of checkpoint therapy response and to identify targets for cancer vaccines and adoptive T cell therapies. For more general information, see the `manuscript published in Genome Medicine <http://www.genomemedicine.com/content/8/1/11>`_.
 
 .. toctree::