Table of Contents Research Proposal: Near-linear exact pairwise alignmentAbstract Introduction and current state of research in the field Goals of the thesisImpact Progress to date Detailed work planWP1: A*PA v1: initial version WP2: Visualizing aligners WP3: Benchmarking aligners WP4: Theory review WP5: A*PA v2: efficient implementation WP6: Affine costs WP7: Ends-free alignment and mapping WP8: Further extension and open ended research WP9: Thesis writing Publication plan Time schedule Teac...
