Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters.
Did you ever wonder whether your MSA is accurate? Did you know that studies show that approximately 25% of the MSA columns are unreliably aligned? As errors in the MSA might affect your results, identifying them is crucial for the analysis of molecular data.
The GUIDANCE web-server (http://guidance.tau.ac.il) is a powerful and user-friendly tool for assigning a confidence score for each residue, column, and sequence in an alignment and for projecting these scores onto the MSA. The server points to columns and sequences that are unreliably aligned and enables their automatic removal from the MSA, in preparation for downstream analyses. Furthermore, GUIDANCE also provides alternative MSAs which can be useful for downstream analyses.
The workshop will introduce some very basic concepts of sequence alignment and the GUIDANCE web-server.