ArticlePloS one2015
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed.
- Covariance decomposition for distance based species tree estimation.BMC bioinformatics · 2026Article
- New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.Environmental microbiome · 2025Article
- ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication.Molecular biology and evolution · 2025Article
- Evolving fitness and immune escape: a retrospective analysis of SARS-CoV-2 spike protein (2020-2024) using protein language model.Frontiers in immunology · 2025Article
- Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests.Systematic biology · 2023Article
- HexSE: Simulating evolution in overlapping reading frames.Virus evolution · 2023Article
- A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures.PLoS computational biology · 2023Article
- Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence.Nature ecology & evolution · 2023Article
- Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation.Systematic biology · 2022Article
- Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination.PLoS computational biology · 2022Article
- phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.PLoS computational biology · 2022Article
- Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins.PLoS computational biology · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Article
- phastSim: efficient simulation of sequence evolution for pandemic-scale datasets.bioRxiv : the preprint server for biology · 2021Article
- Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.Nature genetics · 2021Article
- Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny.Molecular biology and evolution · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype.Frontiers in microbiology · 2021Article
- A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs.Journal of molecular evolution · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve.
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.