Extending Biopython to combine multiple sequence alignments with the same reference into a Multiple Sequence...

Pairwise alignments (PWAs) are commonly used to compare sequences to a reference. Existing alignment tools provide algorithms to align multiple sequences to a single reference and to merge two sets of aligned sequences; but not to combine individually aligned PWAs with a common reference into a single MSA which preserves their original alignment structure. This is required for certain workflows. One example is aligning multiple sequencing traces with a circular plasmid sequence for validation. Some alignment tools that take into account the circularity of the plasmid sequence return a PWA per sequencing trace. For visualization, all PWAs have to be combined into a single MSA. For this purpose, we developed an algorithm that combines alignments sharing the same reference into an MSA, and implemented it as a classmethod in Biopython's Alignment class.