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spider (version 1.1-2)
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
239
Version
1.1-2
License
GPL
Maintainer
Samuel Brown
Last Published
March 14th, 2012
Functions in spider (1.1-2)
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tajima.K
Calculate Tajima's K index of divergence
rosenberg
Rosenberg's probability of reciprocal monophyly
slideBoxplots
Boxplots across windows
sppDist
Intra and inter-specific distances
nearNeighbour
Measures of identification accuracy
localMinima
Determine thresholds from a density plot
spider-package
Species Identity and Evolution in R
tree.comp
Tree comparisons
plot.haploAccum
Plotting haplotype accumulation curves
paa
Population Aggregate Analysis
slideNucDiag
Sliding nucleotide diagnostics
monophyly
Species monophyly over a tree
rankSlidWin
Rank a 'slidWin' object.
rmSingletons
Detect and remove singletons
read.BOLD
Downloads DNA sequences from the Barcode of Life Database (BOLD)
read.GB
Download sequences from Genbank with metadata.
seqStat
Sequence statistics
slidingWindow
Create windows along an alignment
slideAnalyses
Sliding window analyses
tclust
Clustering by a threshold
titv
Number of pairwise transitions and transversions in an alignment.
threshOpt
Threshold optimisation
nonConDist
Nearest non-conspecific and maximum intra-specific distances
seeBarcode
Create illustrative barcodes
is.ambig
Missing bases in alignments
nucDiag
Nucleotide diagnostics for species alignments
haploAccum
Haplotype accumulation curves
sppDistMatrix
Mean intra- and inter-specific distance matrix
anoteropsis
Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species
sppVector
Species Vectors
dataStat
Taxa statistics
polyBalance
Balance of a phylogenetic tree with polytomies
dolomedes
Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
tiporder
Orders tip labels by their position on the tree.
plot.slidWin
Plot a 'slidWin' object
chaoHaplo
Chao estimator of haplotype number
checkDNA
Check a DNA alignment for missing data