Okay, let's see. The user wants me to look at the Methods section of this article and answer specific questions about the pathway enrichment analysis. I need to go through the Methods section carefully and check each question one by one. First, the question is asking about the tool used for pathway enrichment. In the Methods, under the "Positive Selection Analysis" subsection, it mentions that GO category enrichment was performed using the STRING database online software. So the answer to question 1 is STRING. Next, was a tool version number provided? The Methods section has a "Software Versions" subsection, but it lists versions for tools like Trimmomatic, Trinity, etc. Looking there, I don't see a version number for STRING. So question 2's answer is no. For question 3, what gene set library was queried? The article says "GO category enrichment," so the library is Gene Ontology (GO). Question 4 asks if a background gene list was defined. The Methods don't mention defining a background gene list for the enrichment analysis. The analysis was done on positively selected genes, but there's no detail on the background. So answer is not described. Question 5, what statistical test was used? The Methods state that P values were calculated via χ² test on twice the difference in log likelihoods for the codon models. However, for the pathway enrichment itself, it just says "GO category enrichment among positively selected genes was performed with the STRING database online software." The STRING tool might use a hypergeometric test, but the article doesn't specify which test was used. So the answer is not described. Question 6, was FDR correction used? Again, the Methods don't mention any correction for multiple testing in the pathway enrichment analysis. The only mention of correction is in the MIX section where they note no multiple hypothesis correction was performed for the alternate-consensus-run scores. So for question 6, the answer is no, or not described. Since the question is about pathway enrichment, and the article doesn't mention FDR correction there, it's not described. 1. **Tool used for pathway enrichment analysis**: STRING database online software. 2. **Tool version number provided**: Not described. 3. **Gene set library queried**: Gene Ontology (GO) categories. 4. **Background gene list defined**: Not described. 5. **Statistical test used**: Not explicitly described (only mentions P values calculated via χ² test for codon models, not the enrichment analysis itself). 6. **False discovery rate (FDR) correction**: Not described. --- **Table Summary** | Question | Answer | |----------|--------| | 1. Tool used | STRING database online software | | 2. Tool version | Not described | | 3. Gene set library | Gene Ontology (GO) | | 4. Background gene list | Not described | | 5. Statistical test | Not explicitly described | | 6. FDR correction | Not described | **Notes**: - The authors mention using the STRING database for GO category enrichment but do not specify the statistical test or background gene list. - No FDR correction is explicitly stated for the pathway enrichment analysis. - The χ² test referenced in the "Positive Selection Analysis" section pertains to codon model comparisons, not the enrichment analysis itself.