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 "Analysis, identification and visualization of subgroups in genomics" has been published in Briefings in Bioinformatics.
Our paper "A perceptually optimised bivariate visualisation scheme for high-dimensional fold-change data" has been published in Advances in Data Analysis and Classification.