text: user8757: Dear Orthofinder users and BUSCO users,
  Recently, I have assessed 30 genome annotataions using BUSCO with lineage dataset ascomycota_odb10, I got 1100+ complete and single-copy genes. But the orthofinder  only identified 300+ single-copy genes. Aneone else have encountered this similar problem?
  Thanks,
  Yanpeng
  
  user12102: It's hard to say for sure without seeing the exact commands you used. However, Orthofinder identifies/defines single-copy orthologues as those genes present in a single copy in all species being compared in the analysis. If a BUSCO orthologue is present in more than one copy in one of the species being compared (could be multi-copy, could be fragmented etc.), then it won't be recovered as single copy by Orthofinder.
  
original_text: 8757: <p>Dear Orthofinder users and BUSCO users,</p>
  <p>Recently, I have assessed 30 genome annotataions <code>using BUSCO with lineage</code> dataset <code>ascomycota_odb10</code>, I got 1100+ complete and single-copy genes. But the <code>orthofinder</code>  only identified 300+ single-copy genes. Aneone else have encountered this similar problem?</p>
  <p>Thanks,</p>
  <p>Yanpeng</p>
   12102: <p>It's hard to say for sure without seeing the exact commands you used. However, Orthofinder identifies/defines single-copy orthologues as those genes present in a single copy in all species being compared in the analysis. If a BUSCO orthologue is present in more than one copy in one of the species being compared (could be multi-copy, could be fragmented etc.), then it won't be recovered as single copy by Orthofinder.</p>
  