Quick start for USEARCH v8 users

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See also
  What's new in version 9.

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.
 
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.