ArticleBioinformatics (Oxford, England)2012
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed.
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- Arboreal networks and their underlying trees.Journal of mathematical biology · 2026Article
- FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees.Theory of computing systems · 2026Article
- Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface.mSystems · 2025Article
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.iMetaOmics · 2025Article
- Surprising effects of differential loss in genome evolution: the last-one-out.FEMS microbiology letters · 2025Article
- Article
- Complete xylan utilization pathway and regulation mechanisms involved in marine algae degradation by cosmopolitan marine and human gut microbiota.The ISME journal · 2025Article
- Profiling lateral gene transfer events in the human microbiome using WAAFLE.Nature microbiology · 2025Article
- Predicting horizontal gene transfers with perfect transfer networks.Algorithms for molecular biology : AMB · 2024Article
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Relative timing information and orthology in evolutionary scenarios.Algorithms for molecular biology : AMB · 2023Article
- xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes.BMC bioinformatics · 2023Article
- Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.The ISME journal · 2023Article
- HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.Nucleic acids research · 2023Article
- virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method.Life (Basel, Switzerland) · 2022Article
- Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses.Life (Basel, Switzerland) · 2022Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
motivationGene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.
resultsWe present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods. AVAILABILITY: Our programs can be freely downloaded from http://compbio.mit.edu/ranger-dtl/.
Indexed as
Identifiers
What OpenQuestion holds
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.