| anoteropsis | Cytochrome oxidase I (COI) sequences of New Zealand... |
| bestCloseMatch | Measures of identification accuracy |
| blockAlignment | Make all sequences the same length |
| cgraph | Complete graph |
| chaoHaplo | Chao estimator of haplotype number |
| checkDNA | Check a DNA alignment for missing data |
| dataStat | Taxa statistics |
| dolomedes | Cytochrome oxidase I (COI) sequences of New Zealand... |
| haploAccum | Haplotype accumulation curves |
| heatmapSpp | Visualise a distance matrix using a heatmap |
| is.ambig | Missing bases in alignments |
| localMinima | Determine thresholds from a density plot |
| maxInDist | Nearest non-conspecific and maximum intra-specific distances |
| minInDist | Nearest non-conspecific and maximum intra-specific distances |
| monophyly | Species monophyly over a tree |
| monophylyBoot | Species monophyly over a tree |
| nearNeighbour | Measures of identification accuracy |
| nonConDist | Nearest non-conspecific and maximum intra-specific distances |
| nucDiag | Nucleotide diagnostics for species alignments |
| ordinDNA | Calculates a Principal Components Ordination of genetic... |
| paa | Population Aggregate Analysis |
| plot.haploAccum | Plotting haplotype accumulation curves |
| plot.ordinDNA | Plot an 'ordinDNA' object |
| plot.slidWin | Plot a 'slidWin' object |
| polyBalance | Balance of a phylogenetic tree with polytomies |
| rankSlidWin | Rank a 'slidWin' object. |
| read.BOLD | Downloads DNA sequences from the Barcode of Life Database... |
| read.GB | Download sequences from Genbank with metadata. |
| rmSingletons | Detect and remove singletons |
| rnucDiag | Nucleotide diagnostics for species alignments |
| rosenberg | Rosenberg's probability of reciprocal monophyly |
| salticidae | Cytochrome oxidase I (COI) sequences of world-wide species of... |
| sarkar | Dummy sequences illustrating the categories of diagnostic... |
| search.BOLD | Downloads DNA sequences from the Barcode of Life Database... |
| seeBarcode | Create illustrative barcodes |
| seqStat | Sequence statistics |
| slideAnalyses | Sliding window analyses |
| slideBoxplots | Boxplots across windows |
| slideNucDiag | Sliding nucleotide diagnostics |
| slidingWindow | Create windows along an alignment |
| spider-package | Species Identity and Evolution in R |
| sppDist | Intra and inter-specific distances |
| sppDistMatrix | Mean intra- and inter-specific distance matrix |
| sppVector | Species Vectors |
| stats.BOLD | Downloads DNA sequences from the Barcode of Life Database... |
| tajima.K | Calculate Tajima's K index of divergence |
| tclust | Clustering by a threshold |
| threshID | Measures of identification accuracy |
| threshOpt | Threshold optimisation |
| tiporder | Orders tip labels by their position on the tree. |
| titv | Number of pairwise transitions and transversions in an... |
| tree.comp | Tree comparisons |
| woodmouse | Cytochrome b Gene Sequences of Woodmice |
