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spider (version 1.1-3)

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

1.1-3

License

GPL

Maintainer

Samuel Brown

Last Published

April 23rd, 2012

Functions in spider (1.1-3)

haploAccum

Haplotype accumulation curves
slideAnalyses

Sliding window analyses
seqStat

Sequence statistics
monophyly

Species monophyly over a tree
anoteropsis

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

Clustering by a threshold
threshOpt

Threshold optimisation
checkDNA

Check a DNA alignment for missing data
plot.slidWin

Plot a 'slidWin' object
nucDiag

Nucleotide diagnostics for species alignments
plot.haploAccum

Plotting haplotype accumulation curves
dolomedes

Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
rosenberg

Rosenberg's probability of reciprocal monophyly
localMinima

Determine thresholds from a density plot
read.BOLD

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

Measures of identification accuracy
read.GB

Download sequences from Genbank with metadata.
tiporder

Orders tip labels by their position on the tree.
sppDist

Intra and inter-specific distances
polyBalance

Balance of a phylogenetic tree with polytomies
slidingWindow

Create windows along an alignment
seeBarcode

Create illustrative barcodes
tajima.K

Calculate Tajima's K index of divergence
is.ambig

Missing bases in alignments
chaoHaplo

Chao estimator of haplotype number
nonConDist

Nearest non-conspecific and maximum intra-specific distances
spider-package

Species Identity and Evolution in R
slideNucDiag

Sliding nucleotide diagnostics
rmSingletons

Detect and remove singletons
paa

Population Aggregate Analysis
tree.comp

Tree comparisons
dataStat

Taxa statistics
sppVector

Species Vectors
titv

Number of pairwise transitions and transversions in an alignment.
rankSlidWin

Rank a 'slidWin' object.
slideBoxplots

Boxplots across windows
sppDistMatrix

Mean intra- and inter-specific distance matrix