I did gene family identification work based on a paper published in 2017. I used the genome data provided in the article and downloaded the same domain annotations from the Pfam website using the provided domain identifiers. I also used HMM software for gene family identification. However, the article did not provide the parameters used. So, I made some adjustments, but the number of gene families did not change, and there is a significant difference compared to the number mentioned in the paper. What could be the reason for this discrepancy?

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