ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach.
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[1] Jan Gorodkin,et al. Multiple structural alignment and clustering of RNA sequences , 2007, Bioinform..
[2] M. Hasegawa,et al. Model of amino acid substitution in proteins encoded by mitochondrial DNA , 1996, Journal of Molecular Evolution.
[3] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[4] Tobias Müller,et al. The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses , 2006, Nucleic Acids Res..
[5] D. Higgins,et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.
[6] Thomas Dandekar,et al. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE , 2008, BMC Research Notes.
[7] Bruno Torrésani,et al. Rate Matrices for Analyzing Large Families of Protein Sequences , 2002, J. Comput. Biol..
[8] Thomas Dandekar,et al. Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. , 2005, RNA.
[9] P. Stadler,et al. LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. , 2012, RNA.
[10] Knut Reinert,et al. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization , 2007, BMC Bioinformatics.
[11] Thomas W H Lui,et al. Empirical models for substitution in ribosomal RNA. , 2003, Molecular biology and evolution.
[12] Sean R. Eddy,et al. Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..
[13] W. Ludwig,et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.
[14] Klaus Peter Schliep,et al. phangorn: phylogenetic analysis in R , 2010, Bioinform..
[15] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[16] Tobias Müller,et al. ProfDist: a tool for the construction of large phylogenetic trees based on profile distances , 2005, Bioinform..
[17] R. Spang,et al. Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. , 2002, Molecular biology and evolution.
[18] Tobias Müller,et al. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. , 2005, RNA.
[19] B. Michot,et al. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. , 1999, Nucleic acids research.
[20] Tobias Müller,et al. ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments , 2008, Bioinform..
[21] S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .
[22] William R. Taylor,et al. The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..
[23] Robert Giegerich,et al. Pure multiple RNA secondary structure alignments: a progressive profile approach , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[24] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[25] M. O. Dayhoff,et al. 22 A Model of Evolutionary Change in Proteins , 1978 .
[26] J. Schultz,et al. ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. , 2009, Molecular phylogenetics and evolution.
[27] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[28] S. Henikoff,et al. Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[29] Rolf Backofen,et al. Backofen R: MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons , 2005 .
[30] G. Gonnet,et al. Exhaustive matching of the entire protein sequence database. , 1992, Science.
[31] J. Schultz,et al. The ITS2 Database , 2012, Journal of visualized experiments : JoVE.
[32] Jorja G. Henikoff,et al. PHAT: a transmembrane-specific substitution matrix , 2000, Bioinform..
[33] J G Henikoff,et al. PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. , 2000, Bioinformatics.
[34] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[35] Tobias Müller,et al. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing , 2006, BMC Bioinformatics.
[36] Thomas Hackl,et al. ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. , 2012, Molecular phylogenetics and evolution.
[37] Takashi Gojobori,et al. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide , 2005, Journal of Molecular Evolution.
[38] Jan Gorodkin,et al. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods , 2014, Methods in Molecular Biology.
[39] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[40] Thomas Dandekar,et al. Distinguishing species. , 2007, RNA.
[41] Rodrigo Lopez,et al. Clustal W and Clustal X version 2.0 , 2007, Bioinform..
[42] Lars Arvestad,et al. Efficient Methods for Estimating Amino Acid Replacement Rates , 2006, Journal of Molecular Evolution.
[43] S. Whelan,et al. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.
[44] A. von Haeseler,et al. A stochastic model for the evolution of autocorrelated DNA sequences. , 1994, Molecular phylogenetics and evolution.
[45] Martin Vingron,et al. Modeling Amino Acid Replacement , 2000, J. Comput. Biol..
[46] David Posada,et al. MODELTEST: testing the model of DNA substitution , 1998, Bioinform..
[47] Matthias Zytnicki,et al. BlastR—fast and accurate database searches for non-coding RNAs , 2011, Nucleic acids research.
[48] Nan Yu,et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.
[49] A. Coleman,et al. The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants , 1997, Journal of Molecular Evolution.
[50] Frank Förster,et al. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees , 2010, Biology Direct.