BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Suchard, M. A & Redelings, B. D Bioinformatics, 22(16):2047–2048, Oxford University Press, 2006.
bibtex   
@Article{suchard06balia,
  author    = {Suchard, Marc A and Redelings, Benjamin D},
  title     = {BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny},
  journal   = {Bioinformatics},
  year      = {2006},
  volume    = {22},
  number    = {16},
  pages     = {2047--2048},
  publisher = {Oxford University Press},
}
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