Species Identity and Evolution in R
Measures of identification accuracy
Make all sequences the same length
Complete graph
Chao estimator of haplotype number
Check a DNA alignment for missing data
Taxa statistics
Haplotype accumulation curves
Visualise a distance matrix using a heatmap
Missing bases in alignments
Determine thresholds from a density plot
Nearest non-conspecific and maximum intra-specific distances
Nearest non-conspecific and maximum intra-specific distances
Species monophyly over a tree
Species monophyly over a tree
Measures of identification accuracy
Nearest non-conspecific and maximum intra-specific distances
Nucleotide diagnostics for species alignments
Calculates a Principal Components Ordination of genetic distances
Population Aggregate Analysis
Plotting haplotype accumulation curves
Plot an 'ordinDNA' object
Plot a 'slidWin' object
Balance of a phylogenetic tree with polytomies
Rank a 'slidWin' object.
Downloads DNA sequences from the Barcode of Life Database (BOLD)
Download sequences from Genbank with metadata.
Detect and remove singletons
Nucleotide diagnostics for species alignments
Rosenberg's probability of reciprocal monophyly
Downloads DNA sequences from the Barcode of Life Database (BOLD)
Create illustrative barcodes
Sequence statistics
Sliding window analyses
Boxplots across windows
Sliding nucleotide diagnostics
Create windows along an alignment
Species Identity and Evolution in R
Intra and inter-specific distances
Mean intra- and inter-specific distance matrix
Species Vectors
Downloads DNA sequences from the Barcode of Life Database (BOLD)
Calculate Tajima's K index of divergence
Clustering by a threshold
Measures of identification accuracy
Threshold optimisation
Orders tip labels by their position on the tree.
Number of pairwise transitions and transversions in an alignment.
Tree comparisons
Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.