{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T14:57:17Z","timestamp":1763564237841,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,8,27]],"date-time":"2022-08-27T00:00:00Z","timestamp":1661558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian National Health and Medical Research Council","award":["APP1186371"],"award-info":[{"award-number":["APP1186371"]}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP190101504"],"award-info":[{"award-number":["DP190101504"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Victorian government infrastructure support fund"},{"name":"Australian Research Council DECRA fellowship","award":["DE220100965"],"award-info":[{"award-number":["DE220100965"]}]},{"name":"Australian National Health and Medical Research CDF Fellowship","award":["APP1159239"],"award-info":[{"award-number":["APP1159239"]}]},{"name":"Australian Government Research Training Program (RTP) scholarships, and S.M.S is supported by a Monash Graduate Excellence Scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https:\/\/github.com\/seansolari\/expam.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac591","type":"journal-article","created":{"date-parts":[[2022,8,26]],"date-time":"2022-08-26T12:01:34Z","timestamp":1661515294000},"page":"4814-4816","source":"Crossref","is-referenced-by-count":2,"title":["expam\u2014high-resolution analysis of metagenomes using distance trees"],"prefix":"10.1093","volume":"38","author":[{"given":"Sean M","family":"Solari","sequence":"first","affiliation":[{"name":"Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC 3168, Australia"},{"name":"Department of Molecular and Translational Science, Monash University , Clayton, VIC 3168, Australia"}]},{"given":"Remy B","family":"Young","sequence":"additional","affiliation":[{"name":"Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC 3168, Australia"},{"name":"Department of Molecular and Translational Science, Monash University , Clayton, VIC 3168, Australia"}]},{"given":"Vanessa R","family":"Marcelino","sequence":"additional","affiliation":[{"name":"Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC 3168, Australia"},{"name":"Department of Molecular and Translational Science, Monash University , Clayton, VIC 3168, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4144-2537","authenticated-orcid":false,"given":"Samuel C","family":"Forster","sequence":"additional","affiliation":[{"name":"Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC 3168, Australia"},{"name":"Department of Molecular and Translational Science, Monash University , Clayton, VIC 3168, Australia"}]}],"member":"286","published-online":{"date-parts":[[2022,8,27]]},"reference":[{"key":"2022101415200762900_btac591-B1","article-title":"Computational methods for strain-level microbial detection in colony and metagenome sequencing data","volume":"11","author":"Anyasi","year":"2020","journal-title":"Front. 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