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yangao07 / abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
MIT License
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Does not accept other characters aside from A, C, T, and G (DNA Sequence) #46

Open kcjavier21 opened 1 year ago

kcjavier21 commented 1 year ago

Hello! I tried to insert other characters/letters aside from A, C, T, and G, but it resulted to letter "N" in MSA.

If I want to align amino acid sequences instead of DNA sequences, is there a way to use other letters?

Thank you!

image

yangao07 commented 1 year ago

pyabpoa does accept aa sequence with parameter "is_aa=True", refer to https://pypi.org/project/pyabpoa/ for more details.

kcjavier21 commented 1 year ago

Okay cool! But can I use other alpha numeric characters. We are planning to align opcode sequences that are converted to alphanumeric characters.

And adding the said parameter gave me this error. image

This is the example1.png.dot. I guess it's because there's no assigned color in line 11 and 15. image