Abstract
Many biological questions rely upon multiple sequence alignments (MSAs) and phylogenetic trees of large datasets. However, accurate MSA estimation is difficult for large datasets, especially when the dataset evolved under high rates of evolution or contains fragmentary sequences.
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References
Edgar, R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5), 1792–1797 (2004)
Finn, R.D., Clements, J., Eddy, S.R.: HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 39, W29–W37 (2011)
Katoh, K., Toh, H.: PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23, 372–374 (2007)
Mirarab, S., Nguyen, N., Wang, L.-S., Guo, S., Kim, J., Warnow, T.: PASTA: ultra-large multiple sequence alignment of nucleotide and amino acid sequences. J. Computational Biology (2015)
Mirarab, S., Nguyen, N., Warnow, T.: SEPP: SATé-Enabled Phylogenetic Placement. In: Proceedings of the Pacific Symposium on Biocomputing, pp. 247–58, January 2012
Mirarab, S., Nguyen, N., Warnow, T.: PASTA: ultra-large multiple sequence alignment. In: Sharan, R. (ed.) RECOMB 2014. LNCS, vol. 8394, pp. 177–191. Springer, Heidelberg (2014)
Price, M.N., Dehal, P.S., Arkin, A.P.: FastTree 2 – approximately maximum-likelihood trees for large alignments. PloS One 5(3), e9490 (2010)
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Sjöding, J., Thompson, J.D., Higgins, D.G.: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(539), October 2011
Stamatakis, A.: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (Oxford, England), pp. 1–2, February 2014
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Nguyen, Np., Mirarab, S., Kumar, K., Warnow, T. (2015). Ultra-Large Alignments Using Ensembles of Hidden Markov Models. In: Przytycka, T. (eds) Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science(), vol 9029. Springer, Cham. https://doi.org/10.1007/978-3-319-16706-0_26
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DOI: https://doi.org/10.1007/978-3-319-16706-0_26
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