{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,29]],"date-time":"2022-03-29T00:48:55Z","timestamp":1648514935402},"reference-count":14,"publisher":"World Scientific Pub Co Pte Lt","issue":"01","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Open Syst. Inf. Dyn."],"published-print":{"date-parts":[[2009,3]]},"abstract":"<jats:p> Distances in biological databases are known not to be ultrametric. Deviations from ultrametricity can however reveal useful features of biodata. In the present study we examine deviations from ultrametricity of the distances between known phage proteins quantified in two senses: (1) the failure of triangles to be isosceles and (2) failure of every point to be the center of any sphere in which it resides. The deviations from these two ultrametric properties undergo qualitative changes as a function of the distance. Below we describe these changes and how they can be observed. We further argue that the distances at which the qualitative changes take place reveal intrinsic scales in the dataset. Such scales are important for choosing threshold values of the distance in various algorithms and reveal natural chunking of the data that can be used to decide clade levels in phage phylogeny. <\/jats:p>","DOI":"10.1142\/s1230161209000062","type":"journal-article","created":{"date-parts":[[2009,3,31]],"date-time":"2009-03-31T03:27:43Z","timestamp":1238470063000},"page":"75-84","source":"Crossref","is-referenced-by-count":0,"title":["Deviations from Ultrametricity in Phage Protein Distances"],"prefix":"10.1142","volume":"16","author":[{"given":"Chad","family":"Wagner","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Salamon","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA"},{"name":"Department of Philosophy, University of California, La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert A.","family":"Edwards","sequence":"additional","affiliation":[{"name":"Department of Computer Science, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182, USA"},{"name":"Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Forest","family":"Rohwer","sequence":"additional","affiliation":[{"name":"Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Salamon","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2012,1,25]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1163"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.16.4529-4535.2002"},{"key":"rf3","volume":"113","author":"Pedulla M. L.","journal-title":"Cell"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1103\/RevModPhys.58.765"},{"key":"rf6","author":"Benzecri J.","journal-title":"Dunod"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.1967.10500922"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025642"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1038\/297197a0"},{"key":"rf10","unstructured":"A.\u00a0Wilson, The Molecular Basis of Evolution, Scientific American\u00a0253 (1985)\u00a0p. 164."},{"key":"rf11","first-page":"3390","volume":"25","author":"Altschul S.","journal-title":"Nucleic Acids Research"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/22.22.4673"},{"key":"rf13","first-page":"164","volume":"5","author":"Felsenstein J.","journal-title":"Cladistics"},{"key":"rf14","volume-title":"PHYLIP (Phylogeny Inference Package), version 3.57 c","author":"Felsenstein J.","year":"1995"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/8.3.275"}],"container-title":["Open Systems &amp; Information Dynamics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S1230161209000062","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T16:22:09Z","timestamp":1565194929000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S1230161209000062"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,3]]},"references-count":14,"journal-issue":{"issue":"01","published-online":{"date-parts":[[2012,1,25]]},"published-print":{"date-parts":[[2009,3]]}},"alternative-id":["10.1142\/S1230161209000062"],"URL":"https:\/\/doi.org\/10.1142\/s1230161209000062","relation":{},"ISSN":["1230-1612","1793-7191"],"issn-type":[{"value":"1230-1612","type":"print"},{"value":"1793-7191","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,3]]}}}