Realignment Methods

Vertical-oriented realignment in MSA tools

This tool cuts the sequences into small sub-sequences and implements alignment based on the divide-and-conquer algorithm.

Realignemnt will be performed in the area of W distance near the cutting point.

Vertical-oriented refinement:

Scan the initial alignment randomly and pick a column containing at least a gap.
Split the initial alignment into two sub-alignments based on the column.
Remove the empty columns in each sub-alignment and realign them.
If the new alignment's accuracy is improved, the new one replaces the initial one.

Until a predefined maximum number of iterations is reached.

This realignment or refinement is particularly beneficial for smaller sets of sequences.
The github of FAMSA

Its vertical-oriented refinement idea is the same as FAMSA.