The bioBakery help forum

ImportError: Bio.Alphabet has been removed from Biopython


I tried running this shortbred command; --goi tonB.faa --ref tutorial_ref_prots.faa --markers mymarkers.faa --tmp example_identify

and I got this error:

Traceback (most recent call last):
File “/home/po44/miniconda3/bin/”, line 51, in
from shortbred_src import process_blast
File “/home/po44/miniconda3/lib/python3.8/site-packages/shortbred_src/”, line 42, in
from Bio.Alphabet import IUPAC
File “/home/po44/miniconda3/lib/python3.8/site-packages/Bio/Alphabet/”, line 20, in
raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see for more information.

Please, how can I resolve this?

Hello - Thanks for the post. It looks like the latest version of biopython (Sept 2020, v1.78) removed the Bio.Alphabet module. If you roll back your version of biopython it should resolve the error. On our end we will modify shortbred to work with the latest version of biopython.

Thank you,