DOI: 10.18129/B9.bioc.fastreeR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see fastreeR.

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Bioconductor version: 3.16

Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.

Author: Anestis Gkanogiannis [aut, cre]

Maintainer: Anestis Gkanogiannis <anestis at>

Citation (from within R, enter citation("fastreeR")):


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biocViews Clustering, Metagenomics, Phylogenetics, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
License GPL-3
Depends R (>= 4.2)
Imports ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils
Suggests BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0)
SystemRequirements Java (>= 8)
Depends On Me
Imports Me
Suggests Me
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