ArticleGenome biology2008
A simple, fast, and accurate method of phylogenomic inference.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 291 papers.
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Who cites it
291 citing papers in PubMed.
- Trial
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- Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function.Nature ecology & evolution · 2026Article
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.eLife · 2025Article
- Genomic analysis of a clinical Mycolicibacterium houstonense isolate reveals dual escalation in adaptability and virulence.BMC microbiology · 2025Article
- A hitchhiker's guide to modern, practical cyanobacterial taxonomy.Journal of phycology · 2025Article
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.bioRxiv : the preprint server for biology · 2025Article
- Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo.bioRxiv : the preprint server for biology · 2025Article
- Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota.Nature plants · 2025Article
- Fast and exact gap-affine partial order alignment with POASTA.Bioinformatics (Oxford, England) · 2024Article
- Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet.bioRxiv : the preprint server for biology · 2024Article
- Comparative Genomics Revealing the Genomic Characteristics ofTropical medicine and infectious disease · 2024Article
- Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review.Foods (Basel, Switzerland) · 2024Review
- Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.Cell host & microbe · 2024Article
- Analyzing microbial evolution through gene and genome phylogenies.Biostatistics (Oxford, England) · 2024Article
- Protein-Coding Gene Families in Prokaryote Genome Comparisons.Methods in molecular biology (Clifton, N.J.) · 2024Article
- VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution.Microbiome · 2023Article
- Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression.Scientific reports · 2023Article
231 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.