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This is the development version of fastreeR; for the stable release version, see fastreeR.

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

fastreeR HTML R Script
Reference Manual PDF


biocViews Clustering, Metagenomics, Phylogenetics, Software
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.4)
Imports ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils
System Requirements Java (>= 8)
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Suggests BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package fastreeR_1.9.0.tar.gz
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macOS Binary (x86_64) fastreeR_1.9.0.tgz
macOS Binary (arm64) fastreeR_1.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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