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An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees |
Developers
Core software: Ádám Novák, István Miklós, Rune Lyngsø, Joe Herman
Structural alignment plugin: Joe Herman, Christopher Challis
RNA structure prediction plugin: Preeti Arunapuram, Ingólfur Eðvarðsson, Michael Golden
Consensus tree plugin: Hrafn Eiríksson, Viktor Jonsson, David Wood
Parallelised MCMCMC: Joe Herman, Hrafn Eiríksson, Viktor Jonsson, David Wood
Website: Ádám Novák, Joe Herman
Special thanks to:
Jotun Hein,
James Anderson,
Zsuzsanna Sükösd,
William Majoros
License
StatAlign is distributed under the GNU General Public License Version 3.0. A copy of the license is available in the package or can be viewed here.Citing StatAlign
If you use StatAlign in your research, please cite the following papers:
Novák Á, Miklós I, Lyngsø R and Hein J (2008) StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics, 24(20):2403-2404. PubMed Open access
Arunapuram P, Edvardsson I, Golden M, Anderson JWJ, Novák Á, Sükösd Z and Hein J (2013) StatAlign 2.0: Combining statistical alignment with RNA secondary structure prediction. Bioinformatics, 29(5):654-655. PubMed
For the StructAlign plugin, cite
Herman JL, Challis CJ, Novák Á, Hein J and Schmidler, SC (2014) Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Molecular Biology and Evolution, 31(9):2251-2266. PubMed MBE website
Herman JL (2019) Enhancing statistical multiple sequence alignment and tree inference using structural information. In Computational Methods in Protein Evolution, Methods in Molecular Biology, T.X. Sikosek ed., Springer, New York, NY PubMed Springer website