ArticleBioinformatics (Oxford, England)2018
RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.
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 57 papers.
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Who cites it
57 citing papers in PubMed.
- Convergence and conflict among telomere-specialized transposons across 60 million years of Drosophilid evolution.Genome research · 2026Article
- Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.Nature communications · 2026Article
- Evolutionary trajectory of microbial sulfur oxidation pathways recapitulates Earth's oxygenation history.Nature communications · 2026Article
- Evolutionary Analysis of Trehalose Breakdown Pathways.Genome biology and evolution · 2026Article
- What impact do new homologs have on detecting interdomain horizontal gene transfer in eukaryotes? A reassessment of Katz (2015).Biology open · 2026Article
- Phylogenetic reconciliation provides new insights into the evolutionary diversification of the glutamine synthetase gene family in seed plants.The FEBS journal · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.The ISME journal · 2026Article
- FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees.Theory of computing systems · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Prevalence and stable acquisition of biogenic amine-synthesizing genes in lactic acid bacteria across diverse niches: implications for food safety and human health.NPJ science of food · 2025Article
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.bioRxiv : the preprint server for biology · 2025Article
- The Evolution of Function in the DNA-Binding Domain of the CRP/FNR Family.Genome biology and evolution · 2025Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Horizontal acquisition of the Type I restriction-modification system enhances bacterial pathogenicity by mediating methylation of transcription factor-encoding genes.Nucleic acids research · 2025Article
- Horizontal Gene Transfer Inference: Gene Presence-Absence Outperforms Gene Trees.Molecular biology and evolution · 2025Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Discovery of a New Starship Transposon Driving the Horizontal Transfer of theMicroorganisms · 2025Article
- Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.Molecular biology and evolution · 2025Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new software is highly scalable and easy to use, and offers many new features not currently available in any other reconciliation program. RANGER-DTL 2.0 has a particular focus on reconciliation accuracy and can account for many sources of reconciliation uncertainty including uncertain gene tree rooting, gene tree topological uncertainty, multiple optimal reconciliations and alternative event cost assignments. RANGER-DTL 2.0 is open-source and written in C++ and Python. Availability and implementation: Pre-compiled executables, source code (open-source under GNU GPL) and a detailed manual are freely available from http://compbio.engr.uconn.edu/software/RANGER-DTL/. 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.