Schematic view of the global haplotype reconstruction. In the global analysis, users can start from the NGS reads and use the program s2f.py to produce a multiple alignment. Alternatively, one can use another tool to produce the alignment and enter the program workflow at a different point. The program dec.py constructs overlapping windows on this alignment and calls diri_sampler on each window for the local haplotype reconstruction. Then, it collects all results from the individual windows and corrects the reads. The set of corrected reads is passed to the programs contain, mm.py and freqEst to reconstruct the global haplotypes and estimate their frequencies.