The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.
Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas; a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option. (The Eagle1 algorithm can be accessed via the --v1 flag.) Eagle v2.3+ supports phasing sequence data with or without a reference and also supports phasing chrX.
