# ImportError: Bio.Alphabet has been removed from Biopython

**URL:** <https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133>\
**Category:** ShortBRED\
**Created:** [October 9, 2020, 4:58pm UTC](https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133 "2020-10-09T16:58:19Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![paulokoroc](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@paulokoroc](https://forum.biobakery.org/u/paulokoroc)\
**Post date:** [October 9, 2020, 4:58pm UTC](https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133/1 "2020-10-09T16:58:19Z")

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Hi,

I tried running this shortbred command;

```auto
shortbred_identify.py --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/shortbred\_identify.py”, line 51, in   
from shortbred\_src import process\_blast  
File “/home/po44/miniconda3/lib/python3.8/site-packages/shortbred\_src/process\_blast.py”, line 42, in   
from Bio.Alphabet import IUPAC  
File “/home/po44/miniconda3/lib/python3.8/site-packages/Bio/Alphabet/ **init**.py”, 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 [https://biopython.org/wiki/Alphabet](https://biopython.org/wiki/Alphabet) for more information.

Please, how can I resolve this?

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**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [October 16, 2020, 5:15pm UTC](https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133/2 "2020-10-16T17:15:29Z")

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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,  
Lauren

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**Author:** ![fine\_Mero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fine_mero/32/497_2.png) [@fine\_Mero](https://forum.biobakery.org/u/fine_Mero)\
**Post date:** [November 27, 2020, 4:51am UTC](https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133/3 "2020-11-27T04:51:58Z")

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The issue would be done by command-line (conda install biopython=1.68)