Package index • fastreeR

VCF

Functions operating on VCF files

vcf2dist(): Calculate distances between samples of a VCF file
vcf2tree(): Generate phylogenetic tree from samples of a VCF file
vcf2istats(): Calculate various per sample statistics from a VCF file
vcf2clusters(): Perform Hierarchical Clustering and tree pruning on samples of VCF file

FASTA

Functions operating on FASTA sequences

fasta2dist(): Calculate distances between sequences of a FASTA file

Distance and tree utilities

dist2tree(): Generate phylogenetic tree from samples of a distance matrix
dist2clusters(): Perform Hierarchical Clustering and tree pruning on a distance matrix
tree2clusters(): Perform Hierarchical Clustering and tree pruning on a phylogenetic tree

Package

fastreeR fastreeR-package: fastreeR: Phylogenetic, Distance and Other Calculations on VCF and Fasta Files