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EpiFusion was introduced as a framework for joint inference of outbreak characteristics using phylogenetic and case incidence data with particle filtering, enabling estimation of effective reproduction numbers. This article provides analysis vignettes using the EpiFusionUtilities R package and a Java implementation, including an added option to input a posterior distribution over phylogenetic trees. 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We recently introduced EpiFusion, a model for joint inference of outbreak characteristics using phylogenetic and case incidence data via particle filtering and demonstrated its usage to infer the effective reproduction number of simulated and real outbreaks. Here we provide a series of vignettes demonstrating data analysis using the EpiFusion Analysis Framework, consisting of the R package EpiFusionUtilities and the Java program in which the model is implemented, including an example using a new feature incorporated since EpiFusion’s last description: the option to provide a phylogenetic tree posterior as the phylogenetic data input to the program. By outlining these examples, we aim to improve the usability of our model, and promote workflow reproducibility and open research.  \nKeywords  \nresearch software, phylodynamics, epidemiology, joint inference, effective reproduction number, infectious disease, modelling, R, java, particle filtering  \nThis article is included in the Bioinformatics  \ngateway.  \nOpen Peer Review  \n\n| Approval Status  |  |  |\n| --- | --- | --- |\n| 1 | 2 | 3 |\n| version 1   \u003Cbr>view view view\u003Cbr>28 Mar 2025 |  |  |\n\n1. Vijaykrishna Dhanasekaran, The University of Hong Kong, Hong Kong, Hong Kong Ruopeng Xie, The University of Hong Kong, Hong Kong, Hong Kong  \n2. Claire Guinat , Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, Toulouse, France  \n3. Leo A Featherstone, The University of Melbourne, Melbourne, Australia  \nAny reports and responses or comments on the  \narticle can be found at the end of the article.  \nCorresponding author: Ciara Judge ([ciara.judge@lshtm.ac.uk](ciara.judge@lshtm.ac.uk))  \nAuthor roles: Judge C: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Brady O:  \nConceptualization, Methodology, Project Administration, Supervision, Writing – Review & Editing; Hill S: Conceptualization, Methodology,  \nProject Administration, Supervision, Writing – Review & Editing Competing interests: No competing interests were disclosed.  \nGrant information: CJ was supported by a Bloomsbury Colleges PhD Studentship and a National University of Ireland Denis Phelan Scholarship. OJB was supported by a UK Medical Research Council Career Development Award (MR/V031112/1) . SCH was supported by a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust (220414/Z/20/Z) [[https://welcome.org/](https://welcome.org/)]. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The","cbCaisa0GooWvWsE","https://ap.wps.com/l/cbCaisa0GooWvWsE","pdf",1742391,32,"English","# Introduction\n## EpiFusion Analysis Framework overview\n## Software components and workflow\n## Data inputs and posterior phylogenetic trees","[{\"question\":\"What problem does the EpiFusion Analysis Framework target?\",\"answer\":\"It enables joint inference of outbreak characteristics by combining phylogenetic information with case incidence data to support epidemiological understanding and disease control goals.\"},{\"question\":\"What tools are included in the framework?\",\"answer\":\"The framework consists of a Java command-line implementation of the EpiFusion model and the EpiFusionUtilities R package for data and output processing.\"},{\"question\":\"What new data input option is demonstrated in this version?\",\"answer\":\"An option is presented to provide a phylogenetic tree posterior as the phylogenetic data input to the program.\"}]","The EpiFusion Analysis Framework - Software tool for joint phylodynamic and epidemiological outbreak analysis - version 1 | PDF",81,[146,150,154,158],{"page_no":8,"url":147,"width":148,"height":149},"https://res-academy.cache.wpscdn.com/upload/kdocshare/2026-11-07/8bf18dba99c6ce75ad78093066f3d30d.webp",983,1272,{"page_no":14,"url":151,"width":152,"height":153},"https://res-academy.cache.wpscdn.com/upload/kdocshare/2026-11-07/ca14d1e496ca41bca246f3edd235f95c.webp",982,1270,{"page_no":81,"url":155,"width":156,"height":157},"https://res-academy.cache.wpscdn.com/upload/kdocshare/2026-11-07/6204863bf6e26b7d72902a5444d9859a.webp",981,1269,{"page_no":19,"url":159,"width":160,"height":161},"https://res-academy.cache.wpscdn.com/upload/kdocshare/2026-11-07/5dfc62a00bf0353bb3c8799bb035ce6d.webp",980,1268]