Thinking...
We need to answer 6 questions regarding pathway enrichment analysis. We have to find explicitly described methods, tools, versions, gene set libraries, background gene list, tests, multiple testing corrections, from Methods section.

Let's carefully parse the Methods.

The Methods section provided includes "Materials and methods" heading, with subheadings "Collections and bioassays", "Gene silencing/bioassays", "Pooling and quantification of samples", "Bioinformatics", "Alignments and population genetics pipeline", "Statistics", and "Supporting information". In this article, they performed population genetics analysis using χ^2 contingency values and weighted gene-wise average scores, with Benjamini-Hochberg FDR for gene-level significance. They mention gene annotations from Vectorbase using BioMart, functional groups categories assigned manually.

They used "Gene annotations were obtained from Vectorbase using BioMart. Functional groups were assigned to the following categories: ..."

In the 'Statistics' section, they say "Descriptive statistics were calculated in R (version 3.0.2). The ratio of variant sites per nucleotide of aligned reads was calculated as follows: binomial probability distributions were performed and hypergeometric tests were calculated; each functional subset was compared to the corresponding group within the set of all coding genes (n = 14,626)."

They also mention "For GSEA, the mitochondrial and redox categories were combined, as several key redox activities occur in proteins localized to mitochondria."

But they didn't mention any enrichment tool names like DAVID, GSEA, Enrichr etc. Wait: In the Methods, they mention "Gene annotations were obtained from Vectorbase using BioMart." This is annotation extraction. For enrichment analysis, they mention performing hypergeometric tests for each functional subset compared to the group within all coding genes (n=14,626). They also mention "For GSEA, the mitochondrial and redox categories were combined". That indicates they used GSEA? Wait: They said "For GSEA, the mitochondrial and redox categories were combined, as several key redox activities occur in proteins localized to mitochondria." They didn't describe performing GSEA itself; they just combined categories for GSEA. But they didn't actually say they performed GSEA.

The only enrichment analysis described is "Descriptive statistics were calculated in R" and "The ratio of variant sites per nucleotide of aligned reads was calculated as follows: binomial probability distributions were performed and hypergeometric tests were calculated; each functional subset was compared to the corresponding group within the set of all coding genes (n = 14,626)."

Thus the tool used is "Not described"? Wait: The question: "What tool was used for pathway enrichment analysis?: List all tools or software packages used (e.g., DAVID, GSEA, Enrichr, etc.) that are explicitly mentioned in the article for enrichment analysis. Do not include tools used only for preprocessing (e.g., Salmon)." The article does not mention any enrichment tools. They mention hypergeometric test and FDR for gene significance but not enrichment.

Thus answer: Not described.

But we need to check if there is any mention of pathway enrichment. Let's read results: They talk about "Functional groups were assigned to the following categories: ...". They used gene set categories manually. They did not use a standard enrichment tool.

Thus we need to answer 6 questions.

- Tool used for pathway enrichment analysis: Not described. Because they didn't mention a tool like DAVID etc.

- Were enrichment tool versions described? Not described.

- Which gene set libraries were used? Not described.

- Did the article describe using a custom or specific background gene list? They used all coding genes (n = 14,626) as background? In the 'Statistics' they mention "Each functional subset was compared to the corresponding group within the set of all coding genes (n = 14,626). This analysis allowed us to identify the gene sets that were enriched compared to similar categories among all coding genes." That indicates they used all coding genes as background. So the answer: Yes.

- What statistical test(s) used? They mention hypergeometric tests: "binomial probability distributions were performed and hypergeometric tests were calculated; each functional subset was compared to the corresponding group within the set of all coding genes." So test: hypergeometric test.

- Was multiple testing correction/FDR applied to enrichment analysis? They mention "For each collection- '_pvalue', weighted average–log(p value) per gene; AvgHexp_Resistant; AvgHexp_Susceptible." They also mention "Statistical significance was determined using the Benjamini-Hochberg False Discovery Rate (FDR, alpha = 0.01) and a cut-off of 4.0 was established for gene-wise averages." This refers to the gene-wise association, not to enrichment analysis. They didn't mention FDR for enrichment. So answer: No.

Thus the table:

| Question | Answer |
But each column must correspond to each question. The user asked: Provide output in table format. We'll provide columns:

- Tool used for pathway enrichment analysis
- Enrichment tool version(s)
- Gene set libraries used
- Custom/background list used
- Statistical tests used
- Multiple testing correction/FDR applied

Now fill accordingly.

Columns:

Tool used: Not described

Enrichment tool version(s): Not described

Gene set libraries: Not described

Custom background list: Yes (the article used all coding genes as background). Wait, the question: "Does the article describe using a custom or specific background gene list for enrichment analysis? Options: Yes, No or Not described." They used all coding genes (n=14,626). That is a specific background list. So Yes.

Statistical tests: hypergeometric test

Multiple testing correction: Not described (they didn't say FDR for enrichment). So "No".

Thus final table:

| Tool used for pathway enrichment analysis | Enrichment tool version(s) | Gene set libraries used | Custom background gene list | Statistical test(s) | Multiple testing correction/FDR applied |
|-------------------------------------------|----------------------------|--------------------------|-----------------------------|---------------------|----------------------------------------|
| Not described | Not described | Not described | Yes | hypergeometric test | No |

Check for other statements: They also mention "For GSEA, the mitochondrial and redox categories were combined, as several key redox activities occur in proteins localized to mitochondria." They mention GSEA but did not perform GSEA; they mention it in context of combining categories for GSEA. But not used.

Thus final answer.
...done thinking.

| What tool was used for pathway enrichment analysis? | Were enrichment tool version(s) described? | Which gene set libraries were used? | Custom or specific background gene list? | What statistical test(s) were used in enrichment analysis? | Was multiple testing correction / FDR applied to enrichment analysis? |
|-----------------------------------------------|---------------------------------------------|-------------------------------------|----------------------------------------|-----------------------------------------------------------|---------------------------------------------------------------|
| Not described                                 | Not described                               | Not described                       | Yes (all coding genes, n = 14,626)     | Hypergeometric test (binomial probability distribution) | No                                                           |