ArticleMolecular biology and evolution2022
SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 62 citations in OpenAlex.
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- A Group 6 LEA Protein Plays Key Roles in Tolerance to Water Deficit, and in Maintaining the Glassy State and Longevity of Seeds.Plant, cell & environment · 2025Article
- Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.Microbiome · 2025Article
- Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms.Plants (Basel, Switzerland) · 2025Article
- Insect Phylogenomics: From Experiment Planning to Post-phylogenetic Analyses.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Transcriptome and Evolutionary Analysis of Pseudotrichomonas keilini, a Free-Living Anaerobic Eukaryote.Genome biology and evolution · 2024Article
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 2024Article
- 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
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- ATP synthase evolution on a cross-braced dated tree of life.Nature communications · 2023Article
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data.Bioinformatics (Oxford, England) · 2023Article
- Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.Systematic biology · 2022Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.PLoS biology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modeling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated data sets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large data sets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31,612 gene families in 1 h using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.
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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.