Tzu-Hao Kuo

I also encountered a similar issue and finally--after some hours--solved it by reinstalling bedtools. The command that helped me was `roary -a`, with which I learned the statuses of dependencies.

Dear Dr. Schliep, Many thanks for the reply. My alignment includes roughly 500 sequences and 330k columns, which looks smaller than 2 billion bases. Let me check some details more...

@KlausVigo, many thanks for the support. Your suggestion just reminded me to check the residue states in my data, and I just found that my nucleotide alignment includes N's, which...