![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| AICgmyc | Calculate AIC values for GMYC objects |
| AICweights | Calculate AIC values for GMYC objects |
| baseContent | Base composition analysis of an alignment |
| best2nullLRT | Calculate likelihood ratio tests on GMYC objects |
| branches.per.tip | Branches leading to each tip |
| branchesFromNode | Return the indices of branches descending from a given node |
| carpo28S | Sequence alignments of _Carpophilus_ species |
| carpoCOI | Sequence alignments of _Carpophilus_ species |
| carpoITS | Sequence alignments of _Carpophilus_ species |
| carpophilus | Sequence alignments of _Carpophilus_ species |
| clustCI.gmyc | Calculate GMYC statistics |
| clustGMYC | Create a species vector from a GMYC object |
| col2string | Converts R colous names to RGB strings |
| compList | Compares two lists |
| compVectorDist | Calculate composition vector distance |
| DNAccf | Cross-correlation of DNA sequences |
| doloGMYC | GMYC results from New Zealand _Dolomedes_ species |
| doloMultGMYC | GMYC results from New Zealand _Dolomedes_ species |
| enzymes | Data frame of restriction endonuclease enzyme names and cutting regions |
| exCon | Evaluation of sequence contamination |
| giveMeThePicture | Make all sequences the same length |
| homoP | Homopolymers in DNA sequences |
| IDunknown | Identifies unknown sequences by comparison against a local library |
| inCon | Evaluation of sequence contamination |
| maxLike.gmyc | Calculate GMYC statistics |
| narrowingWindow | Make all sequences the same length |
| narrowingWindow2 | Make all sequences the same length |
| nodeDesc | Return the descendants of nodes |
| nodeRect | Plots rectangles on nodes |
| nucDiagExptl | Experimental nucleotide diagnostic function for species alignments |
| permDNA | Permutation of DNA sequences |
| phylo2MRP | Create a matrix representing a tree |
| pindel | DNA distance model incorporating alignment gaps |
| plot.simRFLP | Plot an 'simRFLP' object |
| salticidae | Cytochrome oxidase I (COI) sequences of world-wide species of Salticidae |
| satPlot | Saturation plots |
| satPlot2 | Saturation plots |
| screeline | Number of clusters over a range of thresholds |
| search.GB | Searches for and downloads DNA sequences from GenBank |
| seeSegSites | Visualise the informative sites of an alignment |
| simRFLP | Simulation of Restriction Fragment Length Polymorphism analysis |
| sing2multLRT | Calculate likelihood ratio tests on GMYC objects |
| sppEdge | Returns |
| tclust2sppVector | Creates a species vector from the results of tclust. |
| tipToRootDist | Distance from root to tip |