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spider (version 1.1-1)

Species Identity and Evolution in R

Description

A package for the analysis of species limits and DNA barcoding data

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Version

Install

install.packages('spider')

Monthly Downloads

311

Version

1.1-1

License

GPL

Maintainer

Samuel Brown

Last Published

December 27th, 2011

Functions in spider (1.1-1)

checkDNA

Check a DNA alignment for missing data
monophyly

Species monophyly over a tree
slideNucDiag

Sliding nucleotide diagnostics
spider-package

Species Identity and Evolution in R
nearNeighbour

Measures of identification accuracy
anoteropsis

Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species
sppDistMatrix

Mean intra- and inter-specific distance matrix
rosenberg

Rosenberg's probability of reciprocal monophyly
slideAnalyses

Sliding window analyses
paa

Population Aggregate Analysis
dataStat

Taxa statistics
haploAccum

Haplotype accumulation curves
localMinima

Determine thresholds from a density plot
rmSingletons

Detect and remove singletons
chaoHaplo

Chao estimator of haplotype number
titv

Number of pairwise transitions and transversions in an alignment.
nucDiag

Nucleotide diagnostics for species alignments
seeBarcode

Create illustrative barcodes
read.GB

Download sequences from Genbank with metadata.
tajima.K

Calculate Tajima's K index of divergence
tiporder

Orders tip labels by their position on the tree.
is.ambig

Missing bases in alignments
dolomedes

Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
read.BOLD

Downloads DNA sequences from the Barcode of Life Database (BOLD)
polyBalance

Balance of a phylogenetic tree with polytomies
tclust

Clustering by a threshold
rankSlidWin

Rank a 'slidWin' object.
nonConDist

Nearest non-conspecific and maximum intra-specific distances
sppDist

Intra and inter-specific distances
plot.haploAccum

Plotting haplotype accumulation curves
threshOpt

Threshold optimisation
tree.comp

Tree comparisons
seqStat

Sequence statistics
slidingWindow

Create windows along an alignment
sppVector

Species Vectors
slideBoxplots

Boxplots across windows
plot.slidWin

Plot a 'slidWin' object