The recipe produces pairwise alignments with different software
"Aligning sequences" appears to be a well-defined concept - in reality, it is everything but. The differences in the way aligner operate as well as what they are able to report can be radically different. Adding to the complexity even the same tool may report more or less information, various formats depending on the customization that we apply. Sometimes, certain answers can only be obtained if one were to choose to run a very specific software in a specific way.
The recipe provides code that takes two sequences (by default the 1976 Ebola genome and the 2014 Ebola genome) and generates alignments with different methods between the two viral genomes.
In each case the aligner is asked to produce different outputs, hence ending up with several files for each method.
A detailed presentation that explains the steps and rationale for this recipe can be found at:
Please refer to the lecture above for study materials and additional content.