ArticleBioinformatics (Oxford, England)2020
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers, 2 of them syntheses that pooled it.
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Who cites it
158 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice.Nature communications · 2024Trial
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- Dynamic flexibility of the murine gut microbiota during morphine disturbance enables escape from the stable dysbiosis that is associated with addiction-like behavior.Gut microbes · 2026Article
- Gut protist diversity in Eurasian beavers (International journal for parasitology. Parasites and wildlife · 2026Article
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- Cadmium toxicity to the human gut microbiome varies depending on composition.Applied and environmental microbiology · 2026Article
- First survey on the occurrence, subtype distribution and circulation of the enteric protozoan Blastocystis sp. in French broiler chicken farms.Poultry science · 2026Article
- Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.Nature communications · 2026Article
- Occurrence and subtyping of the intestinal protozoanFood and waterborne parasitology · 2026Article
- The genomic history of Streptococcus mutans from the Mesolithic until modern times.Genome biology · 2026Article
- Antibiotic use in early life impairs MAIT cell-mediated immunity in adulthood.The Journal of experimental medicine · 2026Article
- Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.Environmental microbiology · 2026Article
- The vaginal bacteriome of pregnant Rwandan and Kenyan women, unique regional genera associations with preterm birth.BMC microbiology · 2026Article
- Functionally distinct core microbes of Tricholoma matsutake revealed by cross-study analysis.Microbiome · 2026Article
- Temperature alters interactions and keystone taxa in the marine microbiome.The ISME journal · 2026Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWe present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven. AVAILABILITY AND IMPLEMENTATION: Both genesis and gappa are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.