Initially forked from here. Thank you to the awesome binder team!
Part of the Bioinformatics Virtual Coordination Network :)
This module incorporates (wraps) several other programs/repositories, including
Pseudofinder DIAMOND PAML/codeml/pal2nal.pl Muscle BLAST
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
Print the help menu of the DNDS module
pseudofinder.py dnds -h
Run the DNDS module
pseudofinder.py dnds -a testAnnotate_proteome.faa -n testAnnotate_cds.fasta -ra testAnnotate_ref_proteome.faa -rn testAnnotate_ref_cds.fasta