When filling the axes of the alignment matrix, start in the upper left corner and set it to 0. Next, assign a score for each letter in the row or column. Note that there is a penalty for gaps, and ...

For example, if substitutions occur more often than gaps, then researchers tend to repeatedly choose substitutions over gaps when building the sequence alignment and the resulting alignment can ...

A simple statistical test shows that contrary to current practice, the 'gaps' within DNA protein and sequence alignments commonly used in evolutionary biology can provide important information about ...