CRAIC: interactive interrogation of multiple sequence alignment uncertainty
Multiple sequence alignments (MSAs) are often treated as a solved problem. However, ambiguously or incorrectly aligned regions are the source of much error in phylogenetics and comparative genomics. CRAIC is a cross-platform desktop workbench that treats an alignment as a set of hypotheses to be stress-tested. CRAIC uses the posterior match probabilities of a three-state pair hidden Markov model…
We haven't written up this one. bioRxiv has the full story — the link below goes straight to it.
