Backwards compatibility with v8 Version 9 should be mostly backwards compatible
with version 8 as there are relatively few changes to the internal code
compared with previous major version updates. If users run into any
compatibility problems I will update this page with details.
Deprecated The derep_fulllength command is still supported but is deprecated. Use
fastx_uniques for new scripts.
No longer supported uchime_denovo -- Does not
work well with Illumina. Use an old version of usearch if you have 454
reads. uchime_ref -- Replaced by uchime2_ref.