The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
A simple, fast, and accurate method of phylogenomic inference
Open accessAbstract
The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic analysis (AMPHORA) that overcomes the existing bottlenecks limiting large-scale protein phylogenetic inference. We demonstrated its high throughput capabilities and high quality results by constructing a genome tree of 578 bacterial species and by assigning phylotypes to 18,607 protein markers identified in metagenomic data collected from the Sargasso Sea.
Overview
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
Verification
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.
Citations
Cites
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
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Self-citationToward Automatic Reconstruction of a Highly Resolved Tree of Life
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
SAR11 clade dominates ocean surface bacterioplankton communities
Morris, R. M., Rappé, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., Carlson, C. A., & Giovannoni, S. J. (2002) · Nature · doi:10.1038/nature01240 · Cited by 1,129
Phylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698
Research works printed but not linked: 35
- Woese CR, Achenbach L, Rouviere P, Mandelco L: Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst Appl Microbiol. 1991, 14: 364-371. · DOI · Paper page
- Hasegawa M, Hashimoto T: Ribosomal RNA trees misleading?. Nature. 1993, 361: 23-10.1038/361023b0. · DOI · Paper page
- Ludwig W, Klenk H-P: Overview: A phylogenetic backbone and taxonomic framework for procaryotic systematics. Bergey's Manual of Systematic Bacteriology. Edited by: Boone DR, Castenholz RW, Garrity GM. 2000, New York, NY: Springer-Verlag, 1: 49-65. 2
- Loomis WF, Smith DW: Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc Natl Acad Sci USA. 1990, 87: 9093-9097. 10.1073/pnas.87.23.9093. · DOI
- Lockhart PJ, Howe CJ, Bryant DA, Beanland TJ, Larkum AW: Substitutional bias confounds inference of cyanelle origins from sequence data. J Mol Evol. 1992, 34: 153-162. 10.1007/BF00182392. · DOI · Paper page
- Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF: A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 2000, 290: 972-977. 10.1126/science.290.5493.972. · DOI · Paper page
- Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ: Universal trees based on large combined protein sequence data sets. Nat Genet. 2001, 28: 281-285. 10.1038/90129. · DOI · Paper page
- Delsuc F, Brinkmann H, Philippe H: Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005, 6: 361-375. 10.1038/nrg1603. · DOI · Paper page
- Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA: Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. 2005, 1: e65-10.1371/journal.pgen.0010065. · DOI · Paper page
- Badger JH, Eisen JA, Ward NL: Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. Int J Syst Evol Microbiol. 2005, 55: 1021-1026. 10.1099/ijs.0.63510-0. · DOI
- Brocchieri L: Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol. 2001, 59: 27-40. 10.1006/tpbi.2000.1485. · DOI
- Foster PG, Hickey DA: Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol. 1999, 48: 284-290. 10.1007/PL00006471. · DOI · Paper page
- Gatesy J, DeSalle R, Wheeler W: Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol Phylogenet Evol. 1993, 2: 152-157. 10.1006/mpev.1993.1015. · DOI · Paper page
- Eisen JA: Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 1998, 8: 163-167. · DOI · Paper page
- Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17: 540-552. · DOI · Paper page
- Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF: Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000, 289: 1902-1906. 10.1126/science.289.5486.1902. · DOI · Paper page
- Jain R, Rivera MC, Lake JA: Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 1999, 96: 3801-3806. 10.1073/pnas.96.7.3801. · DOI · Paper page
- Morrison DA, Ellis JT: Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa. Mol Biol Evol. 1997, 14: 428-441. · DOI · Paper page
- Williams KP, Sobral BW, Dickerman AW: A robust species tree for the alphaproteobacteria. J Bacteriol. 2007, 189: 4578-4586. 10.1128/JB.00269-07. · DOI · Paper page
- Lerat E, Daubin V, Moran NA: From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biol. 2003, 1: E19-10.1371/journal.pbio.0000019. · DOI · Paper page
- Moran NA: Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA. 1996, 93: 2873-2878. 10.1073/pnas.93.7.2873. · DOI · Paper page
- Maughan H: Rates of molecular evolution in bacteria are relatively constant despite spore dormancy. Evolution. 2007, 61: 280-288. 10.1111/j.1558-5646.2007.00026.x. · DOI
- Kasai H, Watanabe K, Gasteiger E, Bairoch A, Isono K, Yamamoto S, Harayama S: Construction of the gyrB database for the identification and classification of bacteria. Genome Inform Ser Workshop Genome Inform. 1998, 9: 13-21.
- Santos SR, Ochman H: Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol. 2004, 6: 754-759. 10.1111/j.1462-2920.2004.00617.x. · DOI · Paper page
- Huson DH, Auch AF, Qi J, Schuster SC: MEGAN analysis of metagenomic data. Genome Res. 2007, 17: 377-386. 10.1101/gr.5969107. · DOI · Paper page
- Koski LB, Golding GB: The closest BLAST hit is often not the nearest neighbor. J Mol Evol. 2001, 52: 540-542. · DOI · Paper page
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673. · DOI · Paper page
- Smith SW, Overbeek R, Woese CR, Gilbert W, Gillevet PM: The genetic data environment: an expandable GUI for multiple sequence analysis. Comput Appl Biosci. 1994, 10: 671-675.
- Eddy SR: Profile hidden Markov models. Bioinformatics. 1998, 14: 755-763. 10.1093/bioinformatics/14.9.755. · DOI · Paper page
- Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080/10635150390235520. · DOI · Paper page
- Wiens JJ: Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol. 2003, 52: 528-538. 10.1080/10635150390218330. · DOI · Paper page
- Steel M: Phylogenetic diversity and the greedy algorithm. Syst Biol. 2005, 54: 527-529. 10.1080/10635150590947023. · DOI
- Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J: Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 2008, 36: 2230-2239. 10.1093/nar/gkn038. · DOI · Paper page
- Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM: The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 2005, 33: D294-D296. 10.1093/nar/gki038. · DOI · Paper page
- Letunic I, Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007, 23: 127-128. 10.1093/bioinformatics/btl529. · DOI · Paper page
Cited by
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624
Self-citationBayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
(2015) · doi:10.7717/peerj.1165 · Cited by 1,960
Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314
Metadata
- Authors
- Wu, M., & Eisen, J. A.
- Venue
- Genome Biology
- Published
- 2008-10-13
- Volume
- 9
- Issue
- 10
- Pages
- R151-R151
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2139436782
- Cited by
- 507
- References
- 5
- FWCI
- 10.05
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/2.0/ (tdm)
- creativecommons.org/licenses/by/2.0/ (vor)
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A simple, fast, and accurate method of phylogenomic inference. https://app.cochat.ai/papers/10.1186/gb-2008-9-10-r151
- The paper
- Wu, M., & Eisen, J. A. (2008). A simple, fast, and accurate method of phylogenomic inference. Genome Biology. https://doi.org/10.1186/gb-2008-9-10-r151
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
