About fastreeR | Function overview | Compressed VCF input | Installation | Preparation | Allocate RAM and load required libraries | Download sample vcf file | Download sample fasta files | Functions on vcf files | Sample Statistics | Calculate distances from vcf | Histogram of distances | Plot tree from fastreeR::dist2tree | Bootstrapping example | Bootstrap support explained | Interpretation guidance | Reproducibility note | Bootstrap example (small, runnable) | Optional: nicer plotting with ggtree | Command-line examples | JVM / rJava troubleshooting tips | Windowed VCF analysis | Windowed distance matrices | Windowed trees | Plot tree from stats::hclust | Hierarchical Clustering | Functions on fasta files | Calculate distances from fasta | Session Info
Package: fastreeR 2.3.0
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-11 and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.
Authors:
fastreeR_2.3.0.tar.gz
fastreeR_2.3.0.zip(r-4.7)fastreeR_2.3.0.zip(r-4.6)fastreeR_2.3.0.zip(r-4.5)
fastreeR_2.3.0.tgz(r-4.6-any)fastreeR_2.3.0.tgz(r-4.5-any)
fastreeR_2.3.0.tar.gz(r-4.7-any)fastreeR_2.3.0.tar.gz(r-4.6-any)
fastreeR_2.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fastreeR/json (API)
| # Install 'fastreeR' in R: |
| install.packages('fastreeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gkanogiannis/fastreer/issues
On BioConductor:fastreeR-2.3.0(bioc 3.24)fastreeR-2.2.0(bioc 3.23)
phylogeneticsmetagenomicsclusteringopenjdk
Last updated from:a85f8f11a4. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 168 | ||
| linux-devel-x86_64 | OK | 272 | ||
| source / vignettes | OK | 358 | ||
| linux-release-x86_64 | OK | 165 | ||
| macos-release-arm64 | OK | 93 | ||
| macos-oldrel-arm64 | OK | 138 | ||
| windows-devel | OK | 86 | ||
| windows-release | OK | 140 | ||
| windows-oldrel | OK | 95 | ||
| wasm-release | OK | 172 |
Exports:dist2clustersdist2treefasta2disttree2clustersvcf2clustersvcf2distvcf2istatsvcf2tree
Dependencies:apeclidata.tabledigestdynamicTreeCutgluelatticelifecyclemagrittrnlmeR.methodsS3R.ooR.utilsRcpprJavarlangstringistringrvctrs
