ArticleSystematic biology2016
SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.
Article in Systematic biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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
63 citing papers in PubMed.
- Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof).PLoS computational biology · 2026Article
- Episode clustering in phylogenetic networks.Bioinformatics (Oxford, England) · 2026Article
- Analysis of phylogenetic signal in protein language model embeddings.Scientific reports · 2026Article
- WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.Molecular biology and evolution · 2026Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 2025Article
- 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
- CASTER: Direct species tree inference from whole-genome alignments.Science (New York, N.Y.) · 2025Article
- Net rate of lateral gene transfer in marine prokaryoplankton.The ISME journal · 2025Article
- Terraces in species tree inference from gene trees.BMC ecology and evolution · 2024Article
- Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.Systematic biology · 2024Article
- Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.Bioinformatics (Oxford, England) · 2024Article
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- Generation of accurate, expandable phylogenomic trees with uDance.Nature biotechnology · 2024Article
- Median quartet tree search algorithms using optimal subtree prune and regraft.Algorithms for molecular biology : AMB · 2024Article
- Unifying duplication episode clustering and gene-species mapping inference.Algorithms for molecular biology : AMB · 2024Article
- Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem.Algorithms for molecular biology : AMB · 2024Article
- PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets.Molecular biology and evolution · 2023Article
- Phylogenomic branch length estimation using quartets.Bioinformatics (Oxford, England) · 2023Article
3 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
No grant is acknowledged in the PubMed record.
Abstract
We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases.
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.