{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:46Z","timestamp":1772138086342,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,9]],"date-time":"2018-03-09T00:00:00Z","timestamp":1520553600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Spanish Government","award":["BFU2012-33038"],"award-info":[{"award-number":["BFU2012-33038"]}]},{"name":"Spanish Government","award":["BFU2015-63774-P"],"award-info":[{"award-number":["BFU2015-63774-P"]}]},{"name":"Spanish Government","award":["BES-2013-067181"],"award-info":[{"award-number":["BES-2013-067181"]}]},{"name":"Juan de la Cierva postdoctoral fellowship","award":["FPDI-2013-17503"],"award-info":[{"award-number":["FPDI-2013-17503"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-617457-PHYLOCANCER"],"award-info":[{"award-number":["ERC-617457-PHYLOCANCER"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Advances in sequencing technologies have made it feasible to obtain massive datasets for phylogenomic inference, often consisting of large numbers of loci from multiple species and individuals. The phylogenomic analysis of next-generation sequencing (NGS) data requires a complex computational pipeline where multiple technical and methodological decisions are necessary that can influence the final tree obtained, like those related to coverage, assembly, mapping, variant calling and\/or phasing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To assess the influence of these variables we introduce NGSphy, an open-source tool for the simulation of Illumina reads\/read counts obtained from haploid\/diploid individual genomes with thousands of independent gene families evolving under a common species tree. In order to resemble real NGS experiments, NGSphy includes multiple options to model sequencing coverage (depth) heterogeneity across species, individuals and loci, including off-target or uncaptured loci. For comprehensive simulations covering multiple evolutionary scenarios, parameter values for the different replicates can be sampled from user-defined statistical distributions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code, full documentation and tutorials including a \u2018Getting started\u2019 guide are available at http:\/\/github.com\/merlyescalona\/ngsphy<\/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\/bty146","type":"journal-article","created":{"date-parts":[[2018,3,8]],"date-time":"2018-03-08T07:09:05Z","timestamp":1520492945000},"page":"2506-2507","source":"Crossref","is-referenced-by-count":7,"title":["NGSphy: phylogenomic simulation of next-generation sequencing data"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0213-4777","authenticated-orcid":false,"given":"Merly","family":"Escalona","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Genetics and Immunology"}]},{"given":"Sara","family":"Rocha","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Genetics and Immunology"}]},{"given":"David","family":"Posada","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Genetics and Immunology"},{"name":"Biomedical Research Center (CINBIO), University of Vigo Vigo, Spain"},{"name":"Galicia Sur Health Research Institute Vigo, Spain"}]}],"member":"286","published-online":{"date-parts":[[2018,3,9]]},"reference":[{"key":"2023012713015011600_bty146-B1","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1111\/1755-0998.12449","article-title":"Exon capture phylogenomics: efficacy across scales of divergence","volume":"16","author":"Bragg","year":"2016","journal-title":"Mol. 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