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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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Install
install.packages('spider')
Monthly Downloads
365
Version
1.1-3
License
GPL
Maintainer
Samuel Brown
Last Published
April 23rd, 2012
Functions in spider (1.1-3)
Search functions
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