Many teams have significantly improved upon PLINK 1.0’s implementations of various commands and made their work open source. In several cases, their innovations have been integrated into PLINK 1.9; examples include Pahl et al.’s PERMORY algorithm for fast permutation testing [29],Wan et al.’s BOOST software for fast epistasis testing [30],Ueki, Cordell, and Howey’s –fast-epistasis variance correction and joint-effects test [31,32],Taliun, Gamper, and Pattaro’s optimizations to Gabriel et al.’s haplotype block identification algorithm (discussed above) [26], andPascal Pons’s winning submission to the GWAS Speedup logistic regression crowdsourcing contest [33]. (The contest was designed by Po-Ru Loh, run by Babbage Analytics & Innovation and TopCoder, and subsequent analysis and code preparation were performed by Andrew Hill, Ragu Bharadwaj, and Scott Jelinsky. A manuscript is in preparation by these authors and Iain Kilty, Kevin Boudreau, Karim Lakhani and Eva Guinan.)
