Phymlize

Phyml web server for phylogenic analysis

Phymlize is a web server used for phylogenic analysis written in python2 such as what could be found on ATGC website. It is based on Phyml application. Output file could then be visualized through phylogenic tree visualization tool.

Dependencies

Python 2
Flask
Phyml (should be executable through terminal)

Initialization

To launch the server (Back-end)

After installing dependancies and editing mail account information in config.py, type the following commands from 'egn_server' folder:

    $ chmod +x run.py
    $ ./run.py

How to use it (Front-end)

Once the server is up, type the URL displayed in the terminal (after executing the last command) in your browser's URL bar. By default, it should be http://localhost:8084 but may change depending on your flask configuration.

Start an analysis

Upload a phylip file to the 'New' view form, complete input parameters and click on the "save parameter" button.
Confirm input parameter in the 'Run' view and click on the 'Run analysis' button.
You could check anytime the analysis status by clicking on the 'status' button. Please note that there is also two buttons indicator in the top right corner displaying this info.
If you find that you've done a mistake entering input parameter, you could stop analysis and erase all associated file at anytime by clicking on the 'reset' view
Once analysis is done, click on the 'view' view and click on the desired filename to display its content. You could also search for a specific filename in the 'Read' view.

Please refer to Phyml article and website for input information.