code: def aligned_indel_filter(clust, max_internal_indels):
      
  
      ## make into list
      lclust = clust.split()
      
      ## paired or not
      try:
          seq1 = [i.split("nnnn")[0] for i in lclust[1::2]]
          seq2 = [i.split("nnnn")[1] for i in lclust[1::2]]
          intindels1 = [i.rstrip("-").lstrip("-").count("-") for i in seq1]
          intindels2 = [i.rstrip("-").lstrip("-").count("-") for i in seq2]
          intindels = intindels1 + intindels2
          if max(intindels) > max_internal_indels:
              return 1
         
      except IndexError:
          seq1 = lclust[1::2]
          intindels = [i.rstrip("-").lstrip("-").count("-") for i in seq1]
          if max(intindels) > max_internal_indels:
              return 1 
      
      return 0
docs: checks for too many internal indels in muscle aligned clusters