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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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Install
install.packages('spider')
Monthly Downloads
365
Version
1.1-1
License
GPL
Maintainer
Samuel Brown
Last Published
December 27th, 2011
Functions in spider (1.1-1)
Search functions
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