6. Tutorial (Binder)

Pseudofinder introductory slideshow:

Content | Video presentation

Pseudofinder video tutorial:

Content | Video presentation

To start the tutorial, hit the 'launch binder' button below, and follow the commands in 'Walkthrough'

(Initially forked from here. Thank you to the awesome binder team!)

Walkthrough

Print general help menu

pseudofinder.py help

Print the help menu of the Annotate module

pseudofinder.py annotate -h

Run the Annotate module

pseudofinder.py annotate -g test_data/Mycobacterium_leprae_TN.gbff -db test_data/combined_mycobacteria.faa -op testAnnotate

Run the Annotate module, along with the DNDS module

pseudofinder.py annotate -g test_data/Mycobacterium_leprae_TN.gbff -db test_data/combined_mycobacteria.faa -op testAnnotate --diamond -ref test_data/Mycobacterium_tuberculosis_H37Rv.gbff