Question: Orthofinder: orthogroup graph
gravatar for Hypsis
10 weeks ago by
Hypsis0 wrote:


Can someone explain me the edges in red knowing that edges in yellow correspond to RBNH (orthogroup)? (this is a result from Orthofinder_graph.txt for one orthogroup (a), considering an inflation of 1.1, and which is split into two differents orthogroups (b) after clusterisation with an inflation of 1.5.

(a) : {AT1G29760, AT2G34380, MELO3C007187, OS09G36360, POTRI.011G072200, GSVIVG01014151001, GSVIVG01021275001, Solyc02g071900.2, Solyc07g062230.2}

(b): {GSVIVG01014151001, Solyc07g062230.2} & {Solyc02g071900.2, GSVIVG01021275001, AT1G29760, AT2G34380, MELO3C007187, OS09G36360, POTRI.011G072200}

Considering that,

q is connected to h in the orthogroup graph if B'qh > B'qR where R is an RBNH of q

these edges should not exist, no?

Thanks in advance

software error • 204 views
ADD COMMENTlink modified 21 days ago by Biostar ♦♦ 20 • written 10 weeks ago by Hypsis0

It seems that the author of orthofinder does not suggest changing the inflation index. link

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Sishuo Wang140

Hi Sishuo Wang,

I just think there is a mistake in the construction of the graph that could potentially impact the formed orthogroups. So I'm wondering if there is something I'm missing...

edit: the construction of the graph is independent of the inflation parameter.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Hypsis0
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