1. SAFE_POINT triggered on aligning incorrect files
2. Alphabet is not updated on aligning
3. PDB sequences can not be aligned
4. Some sequences are duplicated when there several sequences with same name in alignment
1. SAFE_POINT triggered on aligning incorrect files
2. Alphabet is not updated on aligning
3. PDB sequences can not be aligned
4. Some sequences are duplicated when there several sequences with same name in alignment