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Fix t_coffee alignment with small sequence

Hello, i have one DNA MSA

msa.png

Everything is were i expect to be, except for the second sequence, it's forced to be aligned in the ends. I tried several things (gapopen and extent values, local alignment) but i cannot find the best combination of paremeters in t_coffee to solve this,

thanks

t_coffee msa alignment
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written by cristianrohr768 • cristianrohr768

You may end up having to manually edit the alignment to fix this. That is fine to do as long as it is within reason.

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written by GenoMax GenoMax

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