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Binder for BVCN Pseudo-Finder lesson

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

Binder

Part of the Bioinformatics Virtual Coordination Network :)

This module incorporates (wraps) several other programs/repositories, including

Pseudofinder DIAMOND PAML/codeml/pal2nal.pl Muscle BLAST

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 

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

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