MAC5 is a program which implements MCMC sampling to estimate a phylogenetic tree from a DNA multiple alignment. What differentiates MAC5 from similar programs (e.g. BAMBE, MrBayes) is its use of five-state sequence evolution models as a means to include the gap information when estimating an alignment. Despite vilification of these models in the literature in the past (e.g., Durbin et al., 1998, p. 217), we have found that, in many circumstances, they are useful for improving the precision of topology estimation.
Grainne McGuire and Paul-Michael Agapow
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Gráinne McGuire, Michael C. Denham and David J. Balding
MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps
Bioinformatics (2001) 17 (5): 479-480.