Links

Here are a few links relating to statistical alignment, and especially to joint estimation of trees and alignments. This page is not intended to be an overall survey of the field, nor is it intended to fully credit all the important work that has been done. Nevertheless, in order for this page to be useful, feel free to point out glaring omissions.

Papers

Joint Estimation

1. Lunter GA, Miklós I, Drummond A, Jensen JL, Hein J Bayesian coestimation of phylogeny and sequence alignment BMC Bioinformatics 6:83, 2005    [WWW]
2. Redelings BD and Suchard MA Joint Bayesian Estimation of Alignment and Phylogeny, Systematic Biology, 54(3):401-418, 2005    [PDF]
3. Roland Fleißner, Dirk Metzler and Arndt von Haeseler, Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction. Syst. Biol., 54:548-561, 2005
4. Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006     [PDF]
5. Redelings BD and Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7:40, 2007    [WWW, PDF]

Statistical Multiple alignment

1. Holmes I and Bruno WJ, Evolutionary HMMs: A Bayesian approach to multiple alignment. Bioinformatics 17:802-820, 2001. PDF
2. Holmes I, Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 19 Suppl. 1:i147-i157, 2003 PDF
3. Lunter GA, Drummond AJ, Miklós I, Hein J, Statistical Alignment: Recent Progress, New Applications, and Challenges, chapter in: Rasmus Nielsen (ed), Statistical Methods in Molecular Evolution, 2004. PDF
4. D. Metzler, R. Fleißner, A. Wakolbinger, A. von Haeseler, Stochastic Insertion-Deletion Processes and Statistical Sequence Alignment, in: "Interacting Stochastic Systems" (J. D. Deuschel, A. Greven, eds), pp. 247-267, Springer-Verlag Berlin Heidelberg 2005. PDF

Indel models

1. [TKF1] Thorne JL, Kishino H, Felsenstein J An evolutionary model for maximum likelihood alignment of DNA sequences J. Mol. Evol. 33: 114-124, 1991
2. [TKF2] Thorne JL, Kishino H, Felsenstein J Inching towards reality: An improved likelihood model of sequence evolution J. Mol. Evol. 34: 3-16 1992
3. Miklós I, Lunter GA, and Holmes I A "Long Indel" Model For Evolutionary Sequence Alignment Mol. Biol. Evol. 21(3):529-540, 2004.

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Software

• StatAlign: Statistical Alignment in Java
• Handel: evolutionary alignment & reconstruction with string transducers
• BAli-Phy: Bayesian Alignment and Phylogeny Estimation

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People and Research Groups

• Oxford &c.
  • Jotun Hein [WWW]
  • Gerton A. Lunter [WWW]
  • István Miklós [WWW]
  • Ian Holmes [WWW]
  • Jens L. Jensen [WWW]
  • Alexei Drummond [WWW]
• Vienna &c.
  • Roland Fleißner [WWW???]
  • Dirk Metzler [WWW]
  • Arndt von Haeseler [WWW]
• UCLA &c.
  • Marc A. Suchard [WWW]
  • Benjamin D. Redelings [WWW]