The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Accounting For Alignment Uncertainty in Phylogenomics
Open accessAbstract
Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy.
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Cites
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
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
Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation
Petersen, J. M., Kemper, A., Gruber-Vodicka, H., Cardini, U., van der Geest, M., Kleiner, M., Bulgheresi, S., Mußmann, M., Herbold, C., Seah, B. K. B., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.195 · Cited by 444
Spiralian Phylogeny Informs the Evolution of Microscopic Lineages
Laumer, C. E., Bekkouche, N., Kerbl, A., Goetz, F., Neves, R. C., Sørensen, M. V., Kristensen, R. M., Hejnol, A., Dunn, C. W., Giribet, G., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.06.068 · Cited by 278
Tan, G., Muffato, M., Ledergerber, C., Herrero, J., Goldman, N., Gil, M., & Dessimoz, C. (2015) · Systematic Biology · doi:10.1093/sysbio/syv033 · Cited by 261
A Phylogenomic Solution to the Origin of Insects by Resolving Crustacean-Hexapod Relationships
Schwentner, M., Combosch, D. J., Pakes Nelson, J., & Giribet, G. (2017) · Current Biology · doi:10.1016/j.cub.2017.05.040 · Cited by 211
Metadata
- Authors
- Wu, M., Chatterji, S., & Eisen, J. A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-01-17
- Volume
- 7
- Issue
- 1
- Pages
- e30288
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2021883973
- Cited by
- 205
- References
- 4
- FWCI
- 5.81
- Type
- journal article
- Language
- en
- Open access
- gold
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