What is the most accurate alignment tool?
Unsurprisingly, the best alignment tool will depend on the situation. In our cross-validation tests, CONTRAlign gives statistically significant advantages in pairwise alignment accuracy on average compared to other current tools. However, • for any particular alignment task, any of a number of different alignment tools (see links page) may perform the best; • for particular alignment situations, other alignment algorithms may be better. For instance when using an alignment to identify a small region of local similarity within two long sequences, you’re best off using a local alignment tool (CONTRAlign is fundamentally a global aligner). In general, no matter which tool you use, be cautious about trusting an alignment reported by any automatic alignment program, especially when the sequences have low (<30) percent identity! Return to top.
