| arrangeCompletenessOutput | This function arrange the completeness output of the... |
| arrangePPOutput | This function arrange the phyloprofile output of the... |
| assessBusco | The function to classify the founded ortholog based on its... |
| assessStatus | The function to classify a founded ortholog from its... |
| autofindPriority | The function determines the priority order of a list of taxa... |
| calculateAllCutoff | The function run calculateCutoff in a loop to calculate... |
| calculateBuscoCutoff | The function to calculate the cutoff value based on standard... |
| calculateCutoff | The function calculate all cutoff values for all mode of a... |
| checkArguments | The function to validate the input. If a input is not... |
| checkCompleteness | The function to check completeness of a interested genome... |
| checkPreProcess | Check if the core set was processed with the function... |
| computeOriginal | The function compute the initial original phylogenetic... |
| computeReport | The function take a path to a genome fasta file and its FAS... |
| concanateFiles | After fdogFAS is finished. It will leave in a temporary... |
| correctDomains | For all with the tool checked genomes, fCAT will save the... |
| correctFasta | For every with the tool checked genomes, fCAT will save the... |
| correctFiles | This function run correctPP, correctFasta, correctDomains,... |
| correctPP | For every with the tool checked genomes, fCAT will save the... |
| createAllAnnotation | The function run createAnnotation function in a loop to... |
| createAnnotation | The function creates FAS annotation for the fasta file of a... |
| extractDomains | A domains file can contains lines of many different genomes.... |
| extractFasta | This function extract the sequences of a specific genome from... |
| extractPP | This function takes a phylogenetic profile, which contains... |
| filterIgnore | Determine if a core gene was ignored by the tool because of... |
| getSpec | The function read the fasta file in each core gene and... |
| handleError | A fail running of fCAT's checkCompleteness function will... |
| placeSeed | This function take the path to the interested genome and its... |
| processCoreSet | The function run createAllAnnotation and calculateAllCufoff... |
| recalculateScore | The output of fdogFAS is a phylogenetic profile (pp). But... |
| reportSingle | Create the report of the completeness of a genome based on... |
| runFdog | This function is used as a modul in the function... |
| runFdogBusco | This function is used as a modul in the function... |
| translateReport | Translate the report table into a frequence table, which tell... |
| updateExFasta | fDOG in runFdog or runFdogBusco will be run with option... |
| updateLength | In the score mode "busco" the tool must calculate the length... |
