Package: phylotools 0.2.4
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_0.2.4.tar.gz
phylotools_0.2.4.zip(r-4.5)phylotools_0.2.4.zip(r-4.4)phylotools_0.2.4.zip(r-4.3)
phylotools_0.2.4.tgz(r-4.4-any)phylotools_0.2.4.tgz(r-4.3-any)
phylotools_0.2.4.tar.gz(r-4.5-noble)phylotools_0.2.4.tar.gz(r-4.4-noble)
phylotools_0.2.4.tgz(r-4.4-emscripten)phylotools_0.2.4.tgz(r-4.3-emscripten)
phylotools.pdf |phylotools.html✨
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 3 years agofrom:758d338b2d. Checks:OK: 7. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 16 2024 |
R-4.5-win | OK | Aug 16 2024 |
R-4.5-linux | OK | Aug 16 2024 |
R-4.4-win | OK | Aug 16 2024 |
R-4.4-mac | OK | Aug 16 2024 |
R-4.3-win | OK | Aug 16 2024 |
R-4.3-mac | OK | Aug 16 2024 |
Exports:clean.fasta.namedat2fastadat2phylipget.fasta.nameget.phylip.nameread.fastaread.phyliprename.fastarm.sequence.fastasplit_datsub.taxa.labelsupermat
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 |