Many parameters of the Eagle algorithm can potentially be modified to trade off accuracy and speed. For simplicity, we created a single ––fast mode that roughly doubles Eagle's speed by increasing the maximum SNP block span from 0.3cM to 0.5cM and reducing the comprehensiveness of the second HMM iteration (by reducing its beam search width from P=200 to 100 and only re-phasing the samples processed in the first half of the first HMM iteration).
