msf2sequence sequence_identifier < alignment.msf > sequence.txt
msf2sequence extracts an individual sequence from an MSF file (eg. "alignment.msf") and saves it as a text file (eg. "sequence.txt"). "sequence_identifier" indicates the label next to the sequence in the MSF-file you want to extract.
The MSF file format is explained here. (MSF files can be converted to and from other more popular alignment file formats (such as FASTA) using aligncopy.)