Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult, because they potentially contain a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. The exclusion of heterozygous sites from evolutionary analysis may cause biased and misleading divergence time estimations in closely related taxa. An approach of repeated random haplotype sampling (RRHS) from sequences with multiple unphased heterozygous sites has been shown to successfully integrate heterozygous information into existing phylogenetic programs. The authors are Heidi Lischer, Gerald Heckel and Laurent Excoffier.
The software can be downloaded from here
Lischer HEL, Excoffier E, Heckel G (2014) Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of Microtus
voles. Mol Biol Evol 31(4): 817-831.