Sequence data
Stockholm gap-column trimmer
Remove alignment columns above a chosen unweighted gap fraction and export aligned FASTA.
Your inputs
Start with an exampleYour result
Example resultAa — A small example of your colors.
How it works
Treat dash and period as gaps. Retain columns whose gap count divided by sequence count is at or below the chosen maximum. Concatenate matching sequence blocks.
Columns 2 and 5 in the example have two gaps out of three sequences. At 0.5 they are removed, leaving ACG for each sequence.
Limits
Up to 2000 sequences and 100000 columns within the input limit. Output is aligned FASTA and omits Stockholm annotations. No sequence weighting, conservation model, fragment adjustment or recommended threshold is inferred.