Package: fastreeR 1.11.0

Anestis Gkanogiannis

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

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.

Authors:Anestis Gkanogiannis [aut, cre]

fastreeR_1.11.0.tar.gz
fastreeR_1.11.0.zip(r-4.5)fastreeR_1.11.0.zip(r-4.4)fastreeR_1.9.0.zip(r-4.3)

fastreeR_1.11.0.tar.gz(r-4.5-noble)fastreeR_1.11.0.tar.gz(r-4.4-noble)
fastreeR_1.11.0.tgz(r-4.4-emscripten)fastreeR_1.9.0.tgz(r-4.3-emscripten)
fastreeR.pdf |fastreeR.html✨
fastreeR/json (API)
NEWS

# Install 'fastreeR' in R:
install.packages('fastreeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/gkanogiannis/fastreer/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:fastreeR-1.11.0(bioc 3.21)fastreeR-1.10.0(bioc 3.20)

phylogeneticsmetagenomicsclustering

5.38 score 3 stars 20 scripts 186 downloads 8 exports 19 dependencies

Last updated 23 days agofrom:5904abcce2. Checks:OK: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winOKNov 20 2024
R-4.5-linuxOKNov 20 2024
R-4.4-winOKNov 20 2024
R-4.3-winOKSep 20 2024

Exports:dist2clustersdist2treefasta2disttree2clustersvcf2clustersvcf2distvcf2istatsvcf2tree

Dependencies:apeclidata.tabledigestdynamicTreeCutgluelatticelifecyclemagrittrnlmeR.methodsS3R.ooR.utilsRcpprJavarlangstringistringrvctrs

fastreeR Vignette

Anestis Gkanogiannis

Rendered fromfastreeR_vignette.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-02-09
Started: 2022-03-19