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A model of evolution and structure for multiple sequence alignment.

Löytynoja A, Goldman N. Löytynoja A, et al. Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3913-9. doi: 10.1098/rstb.2008.0170. Philos Trans R Soc Lond B Biol Sci. 2008. PMID: 18852103 Free PMC article.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J. Lunter G, et al. BMC Bioinformatics. 2005 Apr 1;6:83. doi: 10.1186/1471-2105-6-83. BMC Bioinformatics. 2005. PMID: 15804354 Free PMC article.

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

Kim J, Sinha S. Kim J, et al. Bioinformatics. 2007 Feb 1;23(3):289-97. doi: 10.1093/bioinformatics/btl578. Epub 2006 Nov 15. Bioinformatics. 2007. PMID: 17110370

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.

Löytynoja A, Goldman N. Löytynoja A, et al. Science. 2008 Jun 20;320(5883):1632-5. doi: 10.1126/science.1158395. Science. 2008. PMID: 18566285

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA. Wakefield MJ, et al. BMC Bioinformatics. 2005 May 29;6:130. doi: 10.1186/1471-2105-6-130. BMC Bioinformatics. 2005. PMID: 15921531 Free PMC article.

Hetero: a program to simulate the evolution of DNA on a four-taxon tree.

Jermiin LS, Ho SY, Ababneh F, Robinson J, Larkum AW. Jermiin LS, et al. Appl Bioinformatics. 2003;2(3):159-63. Appl Bioinformatics. 2003. PMID: 15130802

Stochastic models of sequence evolution including insertion-deletion events.

Miklós I, Novák A, Satija R, Lyngsø R, Hein J. Miklós I, et al. Stat Methods Med Res. 2009 Oct;18(5):453-85. doi: 10.1177/0962280208099500. Epub 2009 Feb 16. Stat Methods Med Res. 2009. PMID: 19221170

An alternative model of amino acid replacement.

Crooks GE, Brenner SE. Crooks GE, et al. Bioinformatics. 2005 Apr 1;21(7):975-80. doi: 10.1093/bioinformatics/bti109. Epub 2004 Nov 5. Bioinformatics. 2005. PMID: 15531614

REVCOM: a robust Bayesian method for evolutionary rate estimation.

Bordner AJ, Abagyan R. Bordner AJ, et al. Bioinformatics. 2005 May 15;21(10):2315-21. doi: 10.1093/bioinformatics/bti347. Epub 2005 Mar 4. Bioinformatics. 2005. PMID: 15749694

Joint Bayesian estimation of alignment and phylogeny.

Redelings BD, Suchard MA. Redelings BD, et al. Syst Biol. 2005 Jun;54(3):401-18. doi: 10.1080/10635150590947041. Syst Biol. 2005. PMID: 16012107

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