The BVBRC Meta-CATS service.
The meta-CATS tool looks for positions that significantly differ between user-defined groups of sequences. However, biological biases due to covariation, codon biases, and differences in genotype, geography, time of isolation, or others may affect the robustness of the underlying statistical assumptions.
Based on the paper:
Pickett, B. E., et al. "Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes." Virology 447.1-2 (2013): 45-51.