Man pages for JosephCrispell/homoplasyFinder
Tools to identify and plot homoplasies on a phylogenetic tree
| addInconsistentPositionAlignment | Adds nucleotide alignment to right of plotted phylogenetic... |
| addInternalNodeLabels | Adds labels to plotted tree indicating the internal nodes... |
| addScaleBar | Adds a scale bar to plotted phylogenetic tree if requested |
| assignSiteAlleles | Extract site information |
| getInternalNodeCoordinates | Get the X and Y coordinates of each internal node in the... |
| getMaxCoordinates | Get the maximum X and Y coordinates used on current... |
| getTipCoordinates | Get the X and Y coordinates of each tip in the current... |
| getTipSequences | Reads in FASTA file and records which sequences is associated... |
| plotAnnotatedTree | Plotting HomoplasyFinder results |
| readAnnotatedTree | Read in the annotated Newick tree |
| runHomoplasyFinderInJava | Run HomoplasyFinder using Java code |
| runHomoplasyFinderJarTool | Run HomoplasyFinder using Java jar file. Use if you can't get... |
