Commands based on the USEARCH
algorithm, including usearch_global
and usearch_local,
cluster_fast and
cluster_smallmem,, do not have built-in
limits on sequence length. However, the word-counting heuristics and global
alignments (if applicable) made by these commands tend to be ineffective or
computationally expensive when the sequence length exceeds that of a typical
gene, say somewhere around 50,000 letters. If you have a situation where you
feel that one of these commands would be useful with longer sequences, please
email me to discuss.