PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.
Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB. PHYRN: a robust method for phylogenetic analysis of highly divergent sequences. PLoS One. 2012; 7(4):e34261.