Unable to read all alignments in stockholm format : UnicodeDecodeError: 'utf-8'
The last line indicates that this is an encoding problem. Try to see if the function you are using to read the data has an "encoding" parameter that you can set to whatever encoding your file is using. If that doesn't work, you can change the encoding of your file by:


with save as using a text editor of your choice and selecting "UTF8" as the encoding. That would be a quick work-around if you have a small number of files.


or


You can use the codecs library to check and convert file encodings within your code. Here is an example.


Warning: I haven't used Biopython in ages but encountered similar problems with Python in the past.