Maskaligners

Maskaligners are a class of software tools used in bioinformatics, specifically for sequence alignment. They are designed to handle gaps, also known as insertions or deletions, in DNA or protein sequences more effectively than traditional alignment algorithms. The core idea behind maskaligners is to identify and "mask" regions of high similarity or low complexity within sequences before performing the alignment. These masked regions are often considered less informative for determining evolutionary relationships or functional significance. By excluding these areas, maskaligners aim to reduce spurious matches and improve the accuracy of the alignment in more biologically meaningful parts of the sequences. This approach is particularly useful when aligning distantly related sequences or when dealing with repetitive elements. The output of a maskaligner typically includes the aligned sequences with the masked regions indicated, allowing researchers to focus on the informative differences and similarities.