{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:09:56Z","timestamp":1771373396965,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,1,18]],"date-time":"2017-01-18T00:00:00Z","timestamp":1484697600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The initial step in many orthology inference methods is the computationally demanding establishment of all pairwise protein similarities across all analysed proteomes. The quadratic scaling with proteomes has become a major bottleneck. A remedy is offered by the Hieranoid algorithm which reduces the complexity to linear by hierarchically aggregating ortholog groups from InParanoid along a species tree.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have further developed the Hieranoid algorithm in many ways. Major improvements have been made to the construction of multiple sequence alignments and consensus sequences. Hieranoid version 2 was evaluated with standard benchmarks that reveal a dramatic increase in the coverage\/accuracy tradeoff over version 1, such that it now compares favourably with the best methods. The new parallelized cluster mode allows Hieranoid to be run on large data sets in a much shorter timespan than InParanoid, yet at similar accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Perl code freely available at http:\/\/hieranoid.sbc.su.se\/.<\/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\/btw774","type":"journal-article","created":{"date-parts":[[2016,12,8]],"date-time":"2016-12-08T12:05:45Z","timestamp":1481198745000},"page":"1154-1159","source":"Crossref","is-referenced-by-count":27,"title":["Improved orthology inference with Hieranoid 2"],"prefix":"10.1093","volume":"33","author":[{"given":"Mateusz","family":"Kaduk","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden"},{"name":"Science for Life Laboratory (SciLifeLab), Tomtebodavagen 23, Solna, Sweden"}]},{"given":"Erik","family":"Sonnhammer","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden"},{"name":"Science for Life Laboratory (SciLifeLab), Tomtebodavagen 23, Solna, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2017,1,17]]},"reference":[{"key":"2023020205012663800_btw774-B1","doi-asserted-by":"crossref","first-page":"e1000262.","DOI":"10.1371\/journal.pcbi.1000262","article-title":"Phylogenetic and functional assessment of orthologs inference projects and methods","volume":"5","author":"Altenhoff","year":"2009","journal-title":"PLoS Comput. 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