HOG Gene content

[esud1]

Hi,

I am trying to extract the HOGs of several ancestral genomes. However, I noticed that some of these HOGs share the same id, but different gene content. Is this a common occurrence?

Here are some the examples:

I also notice that Gene(1251002106) and Gene(1251002107) [in the first picture] are listed twice at different HOGs with the same ID.

What could be causing this?

[sinamajidian]

Hi Edi, Thanks for reaching out. Could you possibly share the Orthoxml file and species tree here or by email at sina.majidian at gmail.com? I want to check whether a gene ID is repeated in the orthoxml file or not. If not, we need to check how pyham parses the file.

Best, Sina