KaKsAnalysis pipeline crashes when dealing with proteins that have many alanines, threonines, glycines or cysteines

[shelkmike]

By default, MAFFT automatically determines whether a user has provided amino acid sequences or nucleotide sequences. Sometimes, MAFFT mistakes protein sequences for DNA sequences if a protein has many amino acids A, T, G, C.
There were such proteins in my dataset which caused the KaKsAnalysis pipeline to crash.
To fix this error, I had to add "--amino" to the command that runs MAFFT in the source code of the KaKsAnalysis pipeline.

[Huiting120]

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