The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
GUIDANCE: a web server for assessing alignment confidence scores
Open accessAbstract
Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE web-server, a user-friendly, open access tool for the identification of unreliable alignment regions. The web-server accepts as input a set of unaligned sequences. The server aligns the sequences and provides a simple graphic visualization of the confidence score of each column, residue and sequence of an alignment, using a color-coding scheme. The method is generic and the user is allowed to choose the alignment algorithm (ClustalW, MAFFT and PRANK are supported) as well as any type of molecular sequences (nucleotide, protein or codon sequences). The server implements two different algorithms for evaluating confidence scores: (i) the heads-or-tails (HoT) method, which measures alignment uncertainty due to co-optimal solutions; (ii) the GUIDANCE method, which measures the robustness of the alignment to guide-tree uncertainty. The server projects the confidence scores onto the MSA and points to columns and sequences that are unreliably aligned. These can be automatically removed in preparation for downstream analyses. GUIDANCE is freely available for use at http://guidance.tau.ac.il.
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Alignment Uncertainty and Genomic Analysis
Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411
Cited by
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835
Self-citationTan, G., Muffato, M., Ledergerber, C., Herrero, J., Goldman, N., Gil, M., & Dessimoz, C. (2015) · Systematic Biology · doi:10.1093/sysbio/syv033 · Cited by 261
Pitfalls in supermatrix phylogenomics
Philippe, H., Vienne, D. M. D., Ranwez, V., Roure, B., Baurain, D., & Delsuc, F. (2017) · European Journal of Taxonomy · doi:10.5852/ejt.2017.283 · Cited by 173
Horizontal gene transfer constrains the timing of methanogen evolution
Wolfe, J. M., & Fournier, G. P. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0513-7 · Cited by 160
Evolution of sodium channels predates the origin of nervous systems in animals
Liebeskind, B. J., Hillis, D. M., & Zakon, H. H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106363108 · Cited by 149
Metadata
- Authors
- Penn, O., Privman, E., Ashkenazy, H., Landan, G., Graur, D., & Pupko, T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-05-23
- Volume
- 38
- Issue
- Web Server
- Pages
- W23-W28
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1996516710
- Cited by
- 624
- References
- 1
- FWCI
- 9.45
- Type
- journal article
- Language
- en
- Open access
- gold
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