Spectral Sequence Spectrum for an m nucleotide sequence alignment with or without GAPS

This is a library for the alignment of nucleotide sequences.

When the alignment has some GAPS, the procedure FillingGAPS substitutes those GAPS by nucleotides under the criteria of reducing the variance among character patterns.

When the alignment has no GAPS, the procedure SSS computes the Spectral Sequence Spectrum for it.

Observe that, if the alignment has some GAPS and if one wants to compute its Spectral Sequence Spectrum, the procedure FillingGAPS as well as the procedure SSS have to be implemented in that order.

The library includes examples.

See (Hendy and Snir and, 2005) for more information.

REFERENCE

Michael D. Hendy, and Sagi Snir, Hadamard Conjugation for the Kimura 3st Model: Combinatorial Proof using Pathsets, arXiv: q-bio/0505055v2 [q-bio.PE], (2005) doi: 10.1109/TCBB.2007.70227