6 iPhylo CLI

The iPhylo Command-Line Interface (CLI) is an extension of the web-based iPhylo Tree. It operates offline and comes with integrated databases, which can be deployed either locally or on high-performance computing clusters for enhanced performance.

Importantly, the iPhylo CLI can also construct customized taxonomic trees based on a user-defined hierarchical database so the applications of the iPhylo suite can be extended beyond biological and chemical classifications.

The GitHub repository for iPhylo CLI can be accessed via https://github.com/ARise-fox/iPhylo-CLI/

The iPhylo CLI includes four modules:

  1. Phylotree
  2. Chemtree
  3. Chem Online
  4. CSV2Tree

6.1 Set up

Please use the Python 3 environment. The develope and test environment is Python 38.

Please keep your network available for the first load, as well as enough space on your disk (about 2G), as the initial run needs to fetch the online database resources.

6.2 Packages environment

git clone https://github.com/ARise-fox/iPhylo-CLI.git to clone this project to your local directory. Use pip install -r requirements.txt to preload the required packages.