Interface for the FAKII Fragment Assembly Kernel

This document describes the C programming language interface to our FAKII Fragment Assembly Kernel library. Inputs to the Fragment Assembly Kernel are (1) DNA fragment sequences from potentially inaccurate sequencing experiments, and (2) optional constraints on fragment assembly such as known fragment overlaps or relative fragment orientation. Fragment sequence version control is supported. The Fragment Assembly Kernel produces the most probable reconstructions of the original DNA sequence from the fragments, subject to any specified constraints. Each fragment assembly includes multiple sequence alignment and consensus sequences. Multiple sequence alignment editing capabilities are provided to allow manual correction of sequence errors