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Finding all maximal perfect haplotype blocks in linear time

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye
2020 Algorithms for Molecular Biology  
(Advances in bioinformatics and computational biology: 11th Brazilian symposium on bioinformatics, BSB 2018, Niterói, Brazil, October 30 - November 1, 2018, Proceedings, 2018. 10.1007/978-3-030-01722-4  ...  In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows-Wheeler Transform, that is very efficient  ...  Acknowledgements We thank the organizers of DSB 2019 (dsb2019.gitlab.io) for giving us the opportunity to present earlier work in this area and start a discussion from which the present results originated  ... 
doi:10.1186/s13015-020-0163-6 pmid:32055252 pmcid:PMC7008532 fatcat:hksvts5candxxbpa7e53bbf724