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Only 1 gene in HOG in N0.tsv #926
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Hi SunriseTM, That sounds like an issue that shouldn't be occurring, could you send through the N0 file here so we can take a look and resolve the issue, Thanks |
Hi SunriseTM, Thank you for the files. I've discussed this issue with the rest of the team and it's possible that the issue is down to the topology of the species tree which is used to infer the HOGs from each OG tree. It may be that in some cases a missing species is causing the gene tree to present a gene or set of genes as an outlier, which results in a HOG being inferred on the remaining tree and that gene alone. Would it be possible for you to send through a copy of the species tree generated by OrthoFinder and an example of an OG with a single gene HOG (such as OG0000056). Apologies for the slow reply. |
Hi,Jonathan |
Hi SunriseTM, Do you also have the Resolved_Gene_Tree for OG56 Thanks, Laurie |
Hi,Laurie, |
Hi, Laurie
thanks for your great efforts on such a remarkable software on compative genomics. Recently I found that in some HOGs of N0, only 1 gene was found, which makes it not proper to call it a hierrachical ortho“group”. Do you have any idea on that?
Looking forward for your reply!
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