A package for the analysis of species limits and DNA barcoding data. Development area for functions that will eventually be included in spider proper.
|Author||Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank|
|Date of publication||2016-04-01 10:18:47|
|Maintainer||Samuel Brown <firstname.lastname@example.org>|
AICgmyc: Calculate AIC values for GMYC objects
baseContent: Base composition analysis of an alignment
best2nullLRT: Calculate likelihood ratio tests on GMYC objects
branchesFromNode: Return the indices of branches descending from a given node
branches.per.tip: Branches leading to each tip
carpophilus: Sequence alignments of _Carpophilus_ species
clustCI.gmyc: Calculate GMYC statistics
clustGMYC: Create a species vector from a GMYC object
col2string: Converts R colous names to RGB strings
compList: Compares two lists
compVectorDist: Calculate composition vector distance
DNAccf: Cross-correlation of DNA sequences
doloGMYC: GMYC results from New Zealand _Dolomedes_ species
enzymes: Data frame of restriction endonuclease enzyme names and...
exCon: Evaluation of sequence contamination
homoP: Homopolymers in DNA sequences
IDunknown: Identifies unknown sequences by comparison against a local...
narrowingWindow: Make all sequences the same length
nodeDesc: Return the descendants of nodes
nodeRect: Plots rectangles on nodes
nucDiagExptl: Experimental nucleotide diagnostic function for species...
permDNA: Permutation of DNA sequences
phylo2MRP: Create a matrix representing a tree
pindel: DNA distance model incorporating alignment gaps
plot.simRFLP: Plot an 'simRFLP' object
salticidae: Cytochrome oxidase I (COI) sequences of world-wide species of...
satPlot: Saturation plots
screeline: Number of clusters over a range of thresholds
search.GB: Searches for and downloads DNA sequences from GenBank
seeSegSites: Visualise the informative sites of an alignment
simRFLP: Simulation of Restriction Fragment Length Polymorphism...
tclust2sppVector: Creates a species vector from the results of tclust.
tipToRootDist: Distance from root to tip