Man pages for spider
Species Identity and Evolution in R

anoteropsisCytochrome oxidase I (COI) sequences of New Zealand...
blockAlignmentMake all sequences the same length
cgraphComplete graph
chaoHaploChao estimator of haplotype number
checkDNACheck a DNA alignment for missing data
dataStatTaxa statistics
dolomedesCytochrome oxidase I (COI) sequences of New Zealand...
haploAccumHaplotype accumulation curves
heatmapSppVisualise a distance matrix using a heatmap
is.ambigMissing bases in alignments
localMinimaDetermine thresholds from a density plot
monophylySpecies monophyly over a tree
nearNeighbourMeasures of identification accuracy
nonConDistNearest non-conspecific and maximum intra-specific distances
nucDiagNucleotide diagnostics for species alignments
ordinDNACalculates a Principal Components Ordination of genetic...
paaPopulation Aggregate Analysis
plot.haploAccumPlotting haplotype accumulation curves
plot.ordinDNAPlot an 'ordinDNA' object
plot.slidWinPlot a 'slidWin' object
polyBalanceBalance of a phylogenetic tree with polytomies
rankSlidWinRank a 'slidWin' object.
read.BOLDDownloads DNA sequences from the Barcode of Life Database...
read.GBDownload sequences from Genbank with metadata.
rmSingletonsDetect and remove singletons
rosenbergRosenberg's probability of reciprocal monophyly
salticidaeCytochrome oxidase I (COI) sequences of world-wide species of...
sarkarDummy sequences illustrating the categories of diagnostic...
seeBarcodeCreate illustrative barcodes
seqStatSequence statistics
slideAnalysesSliding window analyses
slideBoxplotsBoxplots across windows
slideNucDiagSliding nucleotide diagnostics
slidingWindowCreate windows along an alignment
spider-packageSpecies Identity and Evolution in R
sppDistIntra and inter-specific distances
sppDistMatrixMean intra- and inter-specific distance matrix
sppVectorSpecies Vectors
tajima.KCalculate Tajima's K index of divergence
tclustClustering by a threshold
threshOptThreshold optimisation
tiporderOrders tip labels by their position on the tree.
titvNumber of pairwise transitions and transversions in an...
tree.compTree comparisons
spider documentation built on May 31, 2017, 2:59 a.m.