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Phylogenetic, Distance and Other Calculations on VCF and Fasta Files

Bioconductor version: Release (3.19)

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))


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 1.8.0
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_1.8.0.tar.gz
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macOS Binary (x86_64) fastreeR_1.8.0.tgz
macOS Binary (arm64) fastreeR_1.8.0.tgz
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Source Repository (Developer Access) git clone
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