The library contains routines for reading sequence and similar files, comparing sequences, and printing tracebacks and alignments. Beyond the immediate utility of the programs, they also serve as examples of standalone programs that can be written using the libseqaln library. Chapter 9 is particularly relevant to this software package.
D find distances between two sequences, as a score.
All results are printed on stdout. Errors are printed to stderr. Indels can be one or more letters in length. The scoring parameters associate a score with each of these events. Additional flags are taken by most of the programs.