The Relaxed Phylip Format | Why building supermatrix? | Commonly used DNA barcoding markers | The gene marker's mutation rate | Missing Data | Similar software | Features of Phylotools | The Installation | Functions in phylotools | Creating supermatrix with phylip files | Generate supermatrix with fasta files | Citation | Further reading
This package is hidden from search results because it is not hosted in the universe of the upstream owner
helixcn. To fix this you can add URL: https://phylotastic.r-universe.dev/phylotools to the package DESCRIPTION file. See also theR-universe documentation.Package: phylotools 0.2.5
Jinlong Zhang
phylotools: Phylogenetic Tools for Eco-Phylogenetics
A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.
Authors:
phylotools_0.2.5.tar.gz
phylotools_0.2.5.zip(r-4.7)phylotools_0.2.5.zip(r-4.6)phylotools_0.2.5.zip(r-4.5)
phylotools_0.2.5.tgz(r-4.6-any)phylotools_0.2.5.tgz(r-4.5-any)
phylotools_0.2.5.tar.gz(r-4.7-any)phylotools_0.2.5.tar.gz(r-4.6-any)
phylotools_0.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phylotools/json (API)
| # Install 'phylotools' in R: |
| install.packages('phylotools', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/helixcn/phylotools/issues
Last updated from:b8716a4b9c. Checks:7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 157 | ||
| source / vignettes | OK | 175 | ||
| linux-release-x86_64 | NOTE | 136 | ||
| macos-release-arm64 | NOTE | 90 | ||
| macos-oldrel-arm64 | NOTE | 123 | ||
| windows-devel | NOTE | 72 | ||
| windows-release | NOTE | 105 | ||
| windows-oldrel | NOTE | 68 | ||
| wasm-release | OK | 113 |
Exports:clean.fasta.namedat2fastadat2phylipget.fasta.nameget.phylip.nameread.fastaread.phyliprename.fastarm.sequence.fastasplit_datsub.taxa.labelsupermat
Building supermatrix matrices using the phylotools package
Last update: 2021-03-24
Started: 2021-02-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Phylogenetic tools for building PHYLIP supermatrix and more | phylotools-package phylotools |
| Clean the name of a fasta file | clean.fasta.name |
| Convert and Save sequence data frame to fasta file | dat2fasta |
| Conver the data frame to sequential PHYLIP format file | dat2phylip |
| get the names of all the sequences of fasta file | get.fasta.name |
| get the names of sequences from a PHYLIP file | get.phylip.name |
| Read FASTA file | read.fasta |
| read phylip file | read.phylip |
| Rename the sequences for a fasta file | rename.fasta |
| Delete sequences from fasta file | rm.sequence.fasta |
| grouping the data frame containing sequences and names and generate fasta file | split_dat |
| Substitute the tip labels of a phylogenetic tree | sub.taxa.label |
| Build PHYLIP supermatrix and RAxML partition file using aligned FASTA or PHYLIP files. | supermat |
