Some interesting mutation assessor tools featured at Automated Personal Genome Analysis
CRAVAT
Cancer-Related Analysis of VAriants Toolkit
http://www.cravat.us/
Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool
BMC Genomics. In press
VAAST
http://www.yandell-lab.org/software/vaast.html
(explicit acknowledgement of VAT)
CHASM and SNVBox:
toolkit for detecting biologically important single nucleotide mutations in cancer.
http://www.ncbi.nlm.nih.gov/pubmed/21685053
http://www.chasmsoftware.org