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| CorMut-package | Detect the correlated mutations based on selection pressure |
| biCkaksAA | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biCkaksAA-class | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biCkaksCodon | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biCkaksCodon-class | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biCompare | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biCompare-class | Class "biCompare" |
| biCompare-method | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biCompare-methods | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biCompare.biCkaksAA | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biCompare.biCkaksCodon | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biCompare.biMIAA | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biCompare.biMICodon | biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
| biMIAA | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biMIAA-class | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biMICodon | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| biMICodon-class | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| ckaks | Class "ckaks" |
| ckaks-class | Class "ckaks" |
| ckaks-method | Class "ckaks" |
| ckaksAA | Compute the conditional kaks(conditional selection pressure) among amino mutations |
| ckaksCodon | Compute the conditional kaks(conditional selection pressure) among codons |
| CorMut | Detect the correlated mutations based on selection pressure |
| filterSites | filterSites methods |
| filterSites-method | filterSites methods |
| filterSites-methods | filterSites methods |
| filterSites.ckaks | filterSites methods |
| filterSites.kaksAA | filterSites methods |
| filterSites.kaksCodon | filterSites methods |
| filterSites.MI | filterSites methods |
| ka | Class "kaksCodon" |
| ka-method | Class "kaksAA" |
| ka-method | Class "kaksCodon" |
| kaks | Class "kaksCodon" |
| kaks-method | Class "kaksAA" |
| kaks-method | Class "kaksCodon" |
| kaksAA | Compute kaks for individual amino mutation |
| kaksAA-class | Class "kaksAA" |
| kaksCodon | Compute kaks for individual codon |
| kaksCodon-class | Class "kaksCodon" |
| ks | Class "kaksCodon" |
| ks-method | Class "kaksAA" |
| ks-method | Class "kaksCodon" |
| lod | Class "kaksCodon" |
| lod-method | Class "ckaks" |
| lod-method | Class "kaksAA" |
| lod-method | Class "kaksCodon" |
| method | Class "biCompare" |
| method-method | Class "biCompare" |
| mi | Class "MI" |
| MI-class | Class "MI" |
| mi-method | Class "MI" |
| miAA | Compute the mutual information among individual amino mutations |
| miCodon | Compute the mutual information among codons |
| p.value | Class "MI" |
| p.value-method | Class "MI" |
| plot | Plot methods for CorMut package |
| plot-method | Plot methods for CorMut package |
| plot.biCompare | Plot methods for CorMut package |
| plot.ckaks | Plot methods for CorMut package |
| plot.MI | Plot methods for CorMut package |
| positiveSite01 | Class "biCompare" |
| positiveSite01-method | Class "biCompare" |
| positiveSite02 | Class "biCompare" |
| positiveSite02-method | Class "biCompare" |
| q | Class "kaksCodon" |
| q-method | Class "kaksAA" |
| q-method | Class "kaksCodon" |
| seqFormat | Process the multiple sequence alignment files |
| seqFormat-methods | Process the multiple sequence alignment files |
| seq_num | Class "kaksCodon" |
| seq_num-method | Class "kaksAA" |
| seq_num-method | Class "kaksCodon" |
| show-method | Class "MI" |
| show-method | Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
| show-method | Class "ckaks" |
| show-method | Class "kaksAA" |
| show-method | Class "kaksCodon" |
| state_1 | Class "biCompare" |
| state_1-method | Class "biCompare" |
| state_2 | Class "biCompare" |
| state_2-method | Class "biCompare" |
| statistic_1 | Class "biCompare" |
| statistic_1-method | Class "biCompare" |
| statistic_2 | Class "biCompare" |
| statistic_2-method | Class "biCompare" |