Only 1 gene in HOG in N0.tsv

[sunriseTM]

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!

[Jonathan-Holmes-Bioinformatics]

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

[sunriseTM]

N0.zip
N2.zip

Of course, and I noted more single gene HOG can be also found in other nodes, for example in my analysis, 1027 single HOG exists in N2.tsv. Thanks for your kind check on that.

[Jonathan-Holmes-Bioinformatics]

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.

[sunriseTM]

Hi，Jonathan
Many thanks for your kind work. A file recording species name and gene name is also attached, may helps.
SpeciesTree_rooted_node_labels.txt
SpeciesAndGeneName.tsv.gz
OG0000056_fasta.txt

[lauriebelch]

Hi SunriseTM,

Do you also have the Resolved_Gene_Tree for OG56

Thanks,

Laurie

[sunriseTM]

Hi，Laurie，
It is also attached, hope you proceed well.
OG0000056_tree.txt