Phyutility: A phyloinformatics tool for trees, alignments and molecular data
Open accessAbstract
Summary: Phyutility provides a set of phyloinformatics tools for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database. Availability: Phyutility, including source code, documentation, examples, and executables, is available at http://code.google.com/p/phyutility Contact: stephen.smith@yale.edu
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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 · see citing works
MrBayes 3: Bayesian phylogenetic inference under mixed models
Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 28,956 · see citing works
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
Castresana, J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026334 · Cited by 10,447 · see citing works
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
Morgenstern, B. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh373 · Cited by 234 · see citing works
RadCon: phylogenetic tree comparison and consensus
Thorley, J., & Page, R. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.5.486 · Cited by 129 · see citing works
Testing the phylogenetic stability of early tetrapods
THORLEY, J. L., & WILKINSON, M. (1999) · Journal of Theoretical Biology · doi:10.1006/jtbi.1999.0999 · Cited by 99 · see citing works
Surfection: a new platform for transfected cell arrays
Chang, F. H. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh029 · Cited by 79 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921 · see citing works
Self-citationAssessing the root of bilaterian animals with scalable phylogenomic methods
Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G. W., Edgecombe, G. D., Martinez, P., Baguñà, J., Bailly, X., Jondelius, U., et al. (2009) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2009.0896 · Cited by 747 · see citing works
Self-citationTempo and Mode of Genome Evolution in the Budding Yeast Subphylum
Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.023 · Cited by 619 · see citing works
Error, signal, and the placement of Ctenophora sister to all other animals
Whelan, N. V., Kocot, K. M., Moroz, L. L., & Halanych, K. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1503453112 · Cited by 331 · see citing works
“Leaf-stability indices (55) for each taxon were measured in PhyUtility (56) to identify potentially unstable taxa in each dataset.”
MethodCyanobacteria and the Great Oxidation Event: evidence from genes and fossils
Schirrmeister, B. E., Gugger, M., & Donoghue, P. C. J. (2015) · Palaeontology · doi:10.1111/pala.12178 · Cited by 304 · see citing works
Deep metazoan phylogeny: When different genes tell different stories
Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W. E. G., Nickel, M., Schierwater, B., et al. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.01.010 · Cited by 254 · see citing works
Kayal, E., Bentlage, B., Sabrina Pankey, M., Ohdera, A. H., Medina, M., Plachetzki, D. C., Collins, A. G., & Ryan, J. F. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1142-0 · Cited by 255 · see citing works
Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015) · doi:10.1101/013946 · Cited by 172 · see citing works
Rooting the Animal Tree of Life
Li, Y., Shen, X.-X., Evans, B., Dunn, C. W., & Rokas, A. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab170 · Cited by 146 · see citing works
Self-citationTreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information
Struck, T. H. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s14239 · Cited by 128 · see citing works
Schnitzler, C. E., Pang, K., Powers, M. L., Reitzel, A. M., Ryan, J. F., Simmons, D., Tada, T., Park, M., Gupta, J., Brooks, S. Y., et al. (2012) · BMC Biology · doi:10.1186/1741-7007-10-107 · Cited by 132 · see citing works
Goloboff, P. A., & Szumik, C. A. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.04.003 · Cited by 73 · see citing works
On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?
Bleidorn, C., Podsiadlowski, L., Zhong, M., Eeckhaut, I., Hartmann, S., Halanych, K. M., & Tiedemann, R. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-150 · Cited by 59 · see citing works
Ekman, S., & Blaalid, R. (2011) · Systematic Biology · doi:10.1093/sysbio/syr022 · Cited by 51 · see citing works
- Authors
- Smith, S. A., & Dunn, C. W.
- Affiliations
- Brown University (US)
- Corresponding author
- Smith, Stephen A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-01-28
- Volume
- 24
- Issue
- 5
- Pages
- 715-716
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2149557149
- Semantic Scholar
- 5e410ad025100890560ed7623559470db36a9eba
- Cited by
- 629
- References
- 7
- Citations by year
- 2026: 16 · 2025: 42 · 2024: 39 · 2023: 37 · 2022: 38 · 2021: 79 · 2020: 58 · 2019: 42 · 2018: 27 · 2017: 26 · 2016: 41 · 2015: 34 · 2014: 44 · 2013: 15 · 2012: 21
- FWCI
- 9.52
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0331654)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- phylogenetic tree, molecular alignment, command-line tool, phylogenetic databases, bioinformatics software
- MeSH terms
- Phylogeny, User-Computer Interface, Sequence Alignment, Computational Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
