Reconstruct Perfect Phylogenies from DNA Sequence Data

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Documentation for package ‘perfectphyloR’ version 0.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

perfectphyloR-package	Reconstruct perfect phylogenies from DNA sequence data
createHapMat	Create an object of class 'hapMat'
dCorTest	dCor test for similarity of two matrices
ex_hapMatSmall_data	Example small dataset
ex_hapMat_data	Example dataset
HHGtest	HHG test for association of two distance matrices
MantelTest	Mantel test for association of two distance matirces
perfectphyloR	Reconstruct perfect phylogenies from DNA sequence data
phenoDist	Phenotypic distances
plotDend	Plot reconstructed dendrogram
RandIndexTest	Rand Index Test
rdistMatrix	Rank-based distances between haplotypes in a given partition
reconstructPP	Reconstruct the perfect phylogeny at a given focal SNV
reconstructPPregion	Reconstruct perfect phylogeny sequencce across a region
RVtest	RV test for association of two distance matrices
tdend	True dendrogram object
testAssoDist	Test the association between a comparator distance matrix, and the reconstructed dendrograms across a genomic region
testDendAssoRI	Tests Rand Index between a comparator dendrogram and reconstructed dendrograms
vcftohapMat	Create a 'hapMat' object from variant call format ('vcf') file.