BLASTphylo is an interactive web-tool, which applies BLAST to a given protein/gene sequence, maps the resulting hits onto a given taxonomic tree, and calculates a phylogeny, all in an automated pipeline. Taxonomic and phylogenetic trees are visualized interactively and allow the user to manipulate the tree on demand, e.g. collapsing the taxonomy to a certain taxonomic rank. If used locally please follow the installation instructions below.
BLASTphylo is available as a web-tool an can be accessed here: Visit BLASTphylo
BLASTphylo calculations require local installations of BLAST (suggest: v2.60+), MAFFT (suggest: v7.310) and FastTree (suggest: v2.1.10, linux recommand installation with sudo apt-get install fasttree) .
Check your FastTree installation with fasttree -help if the command is not found check the installation again
with FastTree -help. Depending on your FastTree installation open the /server/external_tools.py file and
change the cmd="fasttree" parameter of def __init__(self, cmd="fasttree", **kwargs): into your FastTree
command.
This project was bootstrapped with Create React App and requires npm (suggest: node v14.15.0, npm v6.14.8) and python (suggest: v3.6.9) for the installation
For example use:
cd <path/to/BLASTphylo>
virtualenv --python=/usr/bin/python3.6 <your-venv>
source <your-venv>/bin/activate
pip3 install -r server/requirements.txt
pip install .
npm install
command will end with found 3 vulnerabilities (2 moderate, 1 high)
Change into the project directory and run
npm run blastphylo. Start the Flask server.
Make sure that all required modules are installed before running the app. Open http://localhost:3000 to open BLASTphylo in the browser. Enable the pop-up-window function for this app.
The project directory folder server/test_examples contains several example data which can be used as an input for BLASTphylo.
For more details about the different features of BLASTphylo switch to the help page in the top right corner of the application.