ArticleBioinformatics (Oxford, England)2018
SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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Who cites it
122 citing papers in PubMed.
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- The Impact of Visible Symptoms of Thallus Damage on the Phycobiota of Mediterranean Epiphytic Lichens.Microbial ecology · 2026Article
- Perennial vegetative strips promote spillover of beneficial soil microorganisms into adjacent crop field.Scientific reports · 2026Article
- From pathogens to partners: temporal and biogeographical patterns in fungal associations of alien trees.The New phytologist · 2026Article
- Taxonomic revision of the genusPersoonia · 2026Article
- Extremotolerant fungi in resinous soils: a unique diversity of generalists and specialized hydrocarbon degraders.BMC microbiology · 2026Article
- Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.Scientific data · 2026Article
- Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.Animal microbiome · 2026Article
- Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use.Molecular ecology resources · 2026Article
- Phosphorus availability modifies the responses of Glomeromycotina and Mucoromycotina to nitrogen addition.Mycorrhiza · 2026Article
- Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.Molecular ecology resources · 2026Article
- Annual Dynamics of Mycobiota in Symptomatic Century-Old Trees ofJournal of fungi (Basel, Switzerland) · 2026Article
- The saprotrophic dimension ofIMA fungus · 2026Article
- Full ribosomal operon sequencing of anaerobic gut fungi (phylumIMA fungus · 2026Article
- Ultramafic specialist lichens persist through flexible symbioses structured by climate-driven filtering and modulated by substrate effects.IMA fungus · 2026Article
- The ambrosial mycobiota ofIMA fungus · 2026Article
- Article
62 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
Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. Results: SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4 GB of data. Availability and implementation: SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions. 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.