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spider (version 1.1-5)
Species Identity and Evolution in R
Description
A package for the analysis of species limits and DNA barcoding data
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Install
install.packages('spider')
Monthly Downloads
330
Version
1.1-5
License
GPL
Maintainer
Samuel Brown
Last Published
November 15th, 2012
Functions in spider (1.1-5)
Search functions
slideNucDiag
Sliding nucleotide diagnostics
anoteropsis
Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species
monophyly
Species monophyly over a tree
titv
Number of pairwise transitions and transversions in an alignment.
tajima.K
Calculate Tajima's K index of divergence
rmSingletons
Detect and remove singletons
read.GB
Download sequences from Genbank with metadata.
rosenberg
Rosenberg's probability of reciprocal monophyly
sarkar
Dummy sequences illustrating the categories of diagnostic nucleotides
polyBalance
Balance of a phylogenetic tree with polytomies
seqStat
Sequence statistics
slidingWindow
Create windows along an alignment
nearNeighbour
Measures of identification accuracy
dataStat
Taxa statistics
seeBarcode
Create illustrative barcodes
sppDist
Intra and inter-specific distances
sppDistMatrix
Mean intra- and inter-specific distance matrix
nucDiag
Nucleotide diagnostics for species alignments
spider-package
Species Identity and Evolution in R
tiporder
Orders tip labels by their position on the tree.
localMinima
Determine thresholds from a density plot
read.BOLD
Downloads DNA sequences from the Barcode of Life Database (BOLD)
plot.slidWin
Plot a 'slidWin' object
rankSlidWin
Rank a 'slidWin' object.
tree.comp
Tree comparisons
threshOpt
Threshold optimisation
plot.haploAccum
Plotting haplotype accumulation curves
slideAnalyses
Sliding window analyses
chaoHaplo
Chao estimator of haplotype number
sppVector
Species Vectors
dolomedes
Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
nonConDist
Nearest non-conspecific and maximum intra-specific distances
tclust
Clustering by a threshold
checkDNA
Check a DNA alignment for missing data
slideBoxplots
Boxplots across windows
haploAccum
Haplotype accumulation curves
paa
Population Aggregate Analysis
is.ambig
Missing bases in alignments