Man pages for dinaIssakova/rgenesconverged
A Package for Estimating Probability of Convergent Evolution from Genomic Data
| areCondSatisfied | areCondSatisfied |
| BLOSUM62 | Object of class phyDat containing sequences for species... |
| convertToAA | convertToAA |
| convSiteData | Get number of convergent sites |
| getAlignment | getAlignment |
| getBranchLength | getBranchLength |
| getConvergent | Find convergent species |
| getf | Get f |
| getm | Get gene length |
| getMostRecentCommonAncestor | getMostRecentCommonAncestor |
| getSeq | getSeq |
| mapLetters | Convert DNA base format |
| matrixtoAAString | matrixtoAAString |
| pam | PAM matrix. |
| primates | Object of class phyDat containing sequences for species... |
| probOfChange | probOfChange |
| probOfChange1PAM | probOfChange1PAM |
| probOfNSitesByChance | Calculate probability of N chance 'convergent' sites |
| probOfSiteConfig | probOfSiteConfig |
| rgenesconvergedPlot | rgenesconvergedPlot |
| shinyRgenesconverged | shinyRgenesconverged |
| smallTree | smallTree: small phylogenetic tree for testing. |
| tree | primates (phylogenetic tree). |
