ArticleBioinformatics (Oxford, England)2018
RecPhyloXML: a format for reconciled gene trees.
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 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- Alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes.Nature communications · 2026Article
- Phylogenetic reconciliation provides new insights into the evolutionary diversification of the glutamine synthetase gene family in seed plants.The FEBS journal · 2026Article
- HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.Molecular biology and evolution · 2025Article
- AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.Bioinformatics (Oxford, England) · 2024Article
- The hagfish genome and the evolution of vertebrates.Nature · 2024Article
- AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth.Science advances · 2023Article
- The monoaminergic system is a bilaterian innovation.Nature communications · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria.Frontiers in microbiology · 2022Article
- GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss.Molecular biology and evolution · 2020Article
- Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc.-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. Availability and implementation: http://phylariane.univ-lyon1.fr/recphyloxml/.
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Registered trials
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.