Realigners based on vertical partitioning
Cut the input sequences into substrings, and once these shorter substrings are realigned, they stitch their alignments together.
In each iteration:
Extract the blocks from the initial alignment based on the columns with the same bases.
Delete all gaps in each block and realign it with Promalign.
Calculate the SP score of the initial block and the new block.
If the score of the new one is higher than the initial, the new block will be the input of the next iteration.
Until no longer improve the SP score of each block.
Test data: Protein (BALIBASE, PREFAB, OXBENCH, HOMSTRAD)
The source code is not publicized.
Split the initial alignment vertically into 3 parts.
Remove the gap characters in the middle part and realign it alone.
Splice the realigned middle parts with the other two initial pieces to obtain a realigned alignment.
Test data: Protein (BALIBASE, OXBENCH, SABmark)
We did not find the source code.
RPfam employs the Simulated Annealing algorithm in iteration.
In each iteration:
Scan the current MSA for badly aligned blocks and compute score of the blocks.
Randomly pick a badly aligned block.
Seek the worst aligned fragment in the block.
Realign the fragment utilizing DP algorithm.
Update the current MSA.
Until the temperature is down to the setting value the iteration ends.
Realignment in MSA tools
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