Five analysis modules will be executed in PGAP after checking and pre-preparation (Supplementary Fig. S1 ). They are cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. Among all these five modules, the cluster analysis of functional genes module is the basis for the whole program, as other modules are dependent on the orthologous clusters' output from cluster analysis of functional genes. As for species evolution analysis, it is dependent on the results from genetic variation analysis of functional genes and orthologous clusters (Supplementary Material ).
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Functional Gene Cluster Analysis Pipeline
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Other organizations : University of Chinese Academy of Sciences, Beijing Institute of Genomics
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Variable analysis
independent variables
- Cluster analysis of functional genes
- Pan-genome profile analysis
- Genetic variation analysis of functional genes
- Species evolution analysis
- Function enrichment analysis of gene clusters
- Orthologous clusters' output from cluster analysis of functional genes
- Results from genetic variation analysis of functional genes and orthologous clusters
- Not explicitly mentioned
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