| after_ortho_format | Formatted output of OrthoMCL. | 
| after_ortho_format_grps | Formatted output of OrthoMCL. | 
| AnalyzeOrthoMCL | Main OrthoMCL Analysis | 
| CalculatePrincipalCoordinates | Show Principal Components Breakdown | 
| FormatAfterOrtho | Format file from output of OrthoMCL algorithm before use in AnalyzeOrthoMCL | 
| FormatMCLFastas | Format all raw GenBank fastas to single OrthoMCL compatible fasta file | 
| joined_mtrx | Final output of join_repset. | 
| joined_mtrx_grps | Final output of join_repset. | 
| JoinRepSeq | Join Representative Sequences | 
| ManhatGrp | Manhattan Plot of All Taxa | 
| mcl_mtrx | Final output of AnalyzeOrthoMCL | 
| mcl_mtrx_grps | Final output of AnalyzeOrthoMCL | 
| PDGPlot | Plot of a PDG and Data with Standard Error Bars | 
| PDGvOG | Number of PDGs vs OGs/PDG | 
| pheno_data | Triglyceride (TAG) content of fruit flies dataset. | 
| PhyDataError | Phylogenetic Tree with Attached Bar Plot and Standard Error Bars | 
| PrintOGSeqs | Print OG Sequences | 
| QQPlotter | QQPlot | 
| RASTtoGBK | Write RAST files to Genbank formats OrthoMCL Analysis | 
| starv_pheno_data | Starvation rate of fruit flies dataset. | 
| SurvAppendMatrix | Append Survival Test Outputs | 
| WriteMCL | Print analyzed matrix |