feature complete and updated for 2022

The original version of this program was released in 2003. It was distributed at https://www.cgl.ucsf.edu for years, but it would occasionally break due to gradual changes in the C++ language. Many years would go by before someone noticed and fixed it.

This version has been updated for 2022. It complies with the modern C++ compilers using the c++11 standard. Several automated tests have also been added. File formats have changed. (MSF files are no longer a dominant file format for sequence alignment. and PDB files have been superseeded by mmCIF and PDBXML). Links are provided to software which can convert between MSF files and FASTA format.