{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T21:37:29Z","timestamp":1773092249615,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1744309"],"award-info":[{"award-number":["IOS-1744309"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"U.S. National Institutes of Health","doi-asserted-by":"crossref","award":["R01-HG006677"],"award-info":[{"award-number":["R01-HG006677"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2019R1A6A1A1007347"],"award-info":[{"award-number":["2019R1A6A1A1007347"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2020M3A9G7103933"],"award-info":[{"award-number":["2020M3A9G7103933"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2021R1C1C102065"],"award-info":[{"award-number":["2021R1C1C102065"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"New Faculty Startup Fund"},{"name":"Creative-Pioneering Researchers Program through Seoul National University"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>PhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments (MSAs). It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF\/GTF files using precomputed tracks or computes and scores MSAs on the fly with MMseqs2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PhyloCSF++ is released under the AGPLv3 license. Binaries and source code are available at https:\/\/github.com\/cpockrandt\/PhyloCSFpp. The software can be installed through bioconda. A variety of tracks can be accessed through ftp:\/\/ftp.ccb.jhu.edu\/pub\/software\/phylocsfpp\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab756","type":"journal-article","created":{"date-parts":[[2021,10,29]],"date-time":"2021-10-29T15:12:04Z","timestamp":1635520324000},"page":"1440-1442","source":"Crossref","is-referenced-by-count":14,"title":["PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1504-3217","authenticated-orcid":false,"given":"Christopher","family":"Pockrandt","sequence":"first","affiliation":[{"name":"Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21211, USA"},{"name":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21205, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8781-9753","authenticated-orcid":false,"given":"Martin","family":"Steinegger","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Seoul National University , Seoul 08826, Republic of Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8859-7432","authenticated-orcid":false,"given":"Steven L","family":"Salzberg","sequence":"additional","affiliation":[{"name":"Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21211, USA"},{"name":"Department of Biomedical Engineering, Johns Hopkins University , Baltimore, MD 21205, USA"},{"name":"Department of Biostatistics, Johns Hopkins University , Baltimore, MD 21205, USA"},{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21211, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,11,4]]},"reference":[{"key":"2023030901055342900_","author":"Galassi","year":"1996"},{"key":"2023030901055342900_","first-page":"1","author":"Jungreis","year":"2020"},{"key":"2023030901055342900_","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023030901055342900_","doi-asserted-by":"crossref","first-page":"i275","DOI":"10.1093\/bioinformatics\/btr209","article-title":"PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions","volume":"27","author":"Lin","year":"2011","journal-title":"Bioinformatics"},{"key":"2023030901055342900_","doi-asserted-by":"crossref","first-page":"2073","DOI":"10.1101\/gr.246462.118","article-title":"Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci","volume":"29","author":"Mudge","year":"2019","journal-title":"Genome Res"},{"key":"2023030901055342900_","author":"Rhie","year":"2020"},{"key":"2023030901055342900_","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12915-018-0564-x","article-title":"Open questions: how many genes do we have?","volume":"16","author":"Salzberg","year":"2018","journal-title":"BMC Biol"},{"key":"2023030901055342900_","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab756\/41729545\/btab756.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/5\/1440\/49448170\/btab756.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/5\/1440\/49448170\/btab756.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,11]],"date-time":"2023-11-11T18:34:01Z","timestamp":1699727641000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/5\/1440\/6420698"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,11,4]]},"references-count":8,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,2,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab756","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.03.10.434297","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,3,1]]},"published":{"date-parts":[[2021,11,4]]}}}