The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.
Phylogeny-aware alignment with PRANK
Abstract
Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary and structural homology are not the same and sequence alignments generated with methods designed for structural matching can be seriously misleading in comparative and phylogenetic analyses. The phylogeny-aware alignment algorithm implemented in the program PRANK has been shown to produce good alignments for evolutionary inferences. Unlike other alignment programs, PRANK makes use of phylogenetic information to distinguish alignment gaps caused by insertions or deletions and, thereafter, handles the two types of events differently. As a by-product of the correct handling of insertions and deletions, PRANK can provide the inferred ancestral sequences as a part of the output and mark the alignment gaps differently depending on their origin in insertion or deletion events. As the algorithm infers the evolutionary history of the sequences, PRANK can be sensitive to errors in the guide phylogeny and violations on the underlying assumptions about the origin and patterns of gaps. These issues are discussed in detail and practical advice for the use of PRANK in evolutionary analysis is provided. The PRANK software and other methods discussed here can be found from the program home page at http://code.google.com/p/prank-msa/.
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Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Clustal W and Clustal X version 2.0
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm404 · Cited by 28,358
Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
Feng, D.-F., & Doolittle, R. F. (1987) · Journal of Molecular Evolution · doi:10.1007/bf02603120 · Cited by 1,883
An algorithm for progressive multiple alignment of sequences with insertions
Löytynoja, A., & Goldman, N. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409137102 · Cited by 907
Self-citationPhylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
Löytynoja, A., & Goldman, N. (2008) · Science · doi:10.1126/science.1158395 · Cited by 802
Minimal Mutation Trees of Sequences
Sankoff, D. (1975) · SIAM Journal on Applied Mathematics · doi:10.1137/0128004 · Cited by 575
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
Liu, K., Raghavan, S., Nelesen, S., Linder, C. R., & Warnow, T. (2009) · Science · doi:10.1126/science.1171243 · Cited by 512
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
Löytynoja, A., & Goldman, N. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-579 · Cited by 439
Self-citationFletcher, W., & Yang, Z. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq115 · Cited by 264
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
Hogeweg, P., & Hesper, B. (1984) · Journal of Molecular Evolution · doi:10.1007/bf02257378 · Cited by 263
Cited by
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf
Yariv, B., Yariv, E., Kessel, A., Masrati, G., Chorin, A. B., Martz, E., Mayrose, I., Pupko, T., & Ben‐Tal, N. (2023) · Protein Science · doi:10.1002/pro.4582 · Cited by 428
Kim, S., Park, J., Yeom, S.-I., Kim, Y.-M., Seo, E., Kim, K.-T., Kim, M.-S., Lee, J. M., Cheong, K., Shin, H.-S., et al. (2017) · Genome Biology · doi:10.1186/s13059-017-1341-9 · Cited by 312
Convergent regulatory evolution and loss of flight in paleognathous birds
Sackton, T. B., Grayson, P., Cloutier, A., Hu, Z., Liu, J. S., Wheeler, N. E., Gardner, P. P., Clarke, J. A., Baker, A. J., Clamp, M., et al. (2019) · Science · doi:10.1126/science.aat7244 · Cited by 291
Freschi, L., Vincent, A. T., Jeukens, J., Emond-Rheault, J.-G., Kukavica-Ibrulj, I., Dupont, M.-J., Charette, S. J., Boyle, B., & Levesque, R. C. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evy259 · Cited by 286
Metadata
- Authors
- Löytynoja, A.
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2013-08-23
- Volume
- 1079
- Pages
- 155-170
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W128985141
- Cited by
- 743
- References
- 17
- FWCI
- 13.96
- Type
- book chapter
- Language
- en
- Open access
- closed
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