Hello, I used clustal omega software to align 401 sequences mitochondrial DNA. However, I had difficulty understanding the manual and the input options. But still I used the following command:
clustalo -i teste_rn -o teste --threads=16 --outfmt=clustal -v --force
I received the following message:
FORCED DEBUG: Potential Problem: sequences (N = 401) don't have same lengths but contain gaps, consider using --dealign
I used the initial command using input = i. I tried to understand the recommended option (--dealign) but I didn't understand how much it could affect my alignment. As I understand it it removes the gaps and standardizes them all to the same size. That's right? Wouldn't that hurt my result? The sequences may have different sizes because each patient has different indels and in the end the different size is normal. I thought using --dealign this would not be considered and my result would be masked. Can someone help me? what is the best option for me?