Package: fastreeR
Type: Package
Title: Phylogenetic, Distance and Other Calculations on VCF and Fasta Files
Version: 2.1.0
Backend: 2.2.0
biocViews: Phylogenetics, Metagenomics, Clustering
Authors@R:
    c(person(given = "Anestis",
             family = "Gkanogiannis",
             role = c("aut", "cre"),
             email = "anestis@gkanogiannis.com",
             comment = c(ORCID = "0000-0002-6441-0688"))
    )
Description: Calculate distances, build phylogenetic trees or 
    perform hierarchical clustering between the samples of a VCF or FASTA file.
    Functions are implemented in Java-11 and called via rJava.
    Parallel implementation that operates directly on the VCF or FASTA file 
    for fast execution.
License: GPL-3
Encoding: UTF-8
Language: en-US
LazyData: false
Depends:
    R (>= 4.4)
Imports: 
    ape,
    data.table,
    dynamicTreeCut,
    methods,
    R.utils,
    rJava,
    stats,
    stringr,
    utils
SystemRequirements: Java (>= 11)
RoxygenNote: 7.3.2
URL: https://github.com/gkanogiannis/fastreeR, 
     https://github.com/gkanogiannis/BioInfoJava-Utils
BugReports: https://github.com/gkanogiannis/fastreeR/issues
Suggests: 
    BiocFileCache,
    BiocStyle,
    ggtree,
    graphics,
    knitr,
    memuse,
    rmarkdown,
    spelling,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/fastreeR
git_branch: devel
git_last_commit: f9dc08c
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
