anoteropsis             Cytochrome oxidase I (COI) sequences of New
                        Zealand _Anoteropsis_ species
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 _Dolomedes_ species
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 distances
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 (BOLD)
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 Salticidae
sarkar                  Dummy sequences illustrating the categories of
                        diagnostic nucleotides
search.BOLD             Downloads DNA sequences from the Barcode of
                        Life Database (BOLD)
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 (BOLD)
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 alignment.
tree.comp               Tree comparisons
woodmouse               Cytochrome b Gene Sequences of Woodmice
