{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:36Z","timestamp":1753875876945,"version":"3.41.2"},"reference-count":102,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T00:00:00Z","timestamp":1746489600000},"content-version":"vor","delay-in-days":131,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Technology and Engineering Solutions of Sandia, LLC"},{"name":"U.S. Department of Energy\u2019s National Nuclear Security Administration","award":["DE-NA0003525"],"award-info":[{"award-number":["DE-NA0003525"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Freely available on GitHub at https:\/\/github.com\/sandialabs\/poplar. Implemented using Python and supported on Linux.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf104","type":"journal-article","created":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T12:00:58Z","timestamp":1746532858000},"source":"Crossref","is-referenced-by-count":0,"title":["Poplar: a phylogenomics pipeline"],"prefix":"10.1093","volume":"5","author":[{"given":"Elizabeth","family":"Koning","sequence":"first","affiliation":[{"name":"Biosecurity and Bioassurance Department, Sandia National Laboratories , Livermore, CA 94550,","place":["United States"]},{"name":"Department of Computer Science, University of Illinois, Urbana-Champaign , Urbana, IL 61801,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arjun","family":"Subedi","sequence":"additional","affiliation":[{"name":"Biosecurity and Bioassurance Department, Sandia National Laboratories , Livermore, CA 94550,","place":["United States"]},{"name":"Department of Computer Science, California State University , Fullerton, CA 92831,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2479-754X","authenticated-orcid":false,"given":"Raga","family":"Krishnakumar","sequence":"additional","affiliation":[{"name":"Biosecurity and Bioassurance Department, Sandia National Laboratories , Livermore, CA 94550,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,5,6]]},"reference":[{"key":"2025061901544296700_vbaf104-B1","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1038\/s41564-018-0261-0","article-title":"Leveraging single-cell genomics to expand the fungal tree of life","volume":"3","author":"Ahrendt","year":"2018","journal-title":"Nat 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