A tool for aligning DNA/RNA sequences and protein sequences.
Swat is a java commandline software based on dynamic programming to calculate optimal local alignments of DNA/RNA sequences and protein sequences.
Documentation:
Please also see our corresponding publication:
Fürstberger A, Maucher M, Kestler HA. Extended pairwise local alignment of wild card DNA/RNA-sequences using dynamic programming. J Stat Comput Simul 85(1): 3-13, 2015. https://doi.org/10.1080/00949655.2014.928294
Our paper "Awakening the HSC: Dynamic Modeling of HSC Maintenance Unravels Regulation of the TP53 Pathway and Quiescence" has been published in Frontiers in Physiology.
Our review article "Concepts in Boolean Network Modeling - What Do They All Mean?" has been published in Computational and Structural Biotechnology Journal.