{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:20:24Z","timestamp":1761895224895},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,1,24]],"date-time":"2011-01-24T00:00:00Z","timestamp":1295827200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-30","type":"journal-article","created":{"date-parts":[[2011,1,25]],"date-time":"2011-01-25T02:16:12Z","timestamp":1295921772000},"source":"Crossref","is-referenced-by-count":8,"title":["iPhy: an integrated phylogenetic workbench for supermatrix analyses"],"prefix":"10.1186","volume":"12","author":[{"given":"Martin O","family":"Jones","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgios D","family":"Koutsovoulos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark L","family":"Blaxter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,1,24]]},"reference":[{"key":"4347_CR1","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1038\/nature08742","volume":"463","author":"JC Regier","year":"2010","unstructured":"Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW: Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010, 463: 1079\u20131083. 10.1038\/nature08742","journal-title":"Nature"},{"key":"4347_CR2","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1038\/nature06614","volume":"452","author":"CW Dunn","year":"2008","unstructured":"Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, S\u00f8rensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G: Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452: 745\u2013749. 10.1038\/nature06614","journal-title":"Nature"},{"key":"4347_CR3","doi-asserted-by":"publisher","first-page":"2451","DOI":"10.1093\/molbev\/msq130","volume":"27","author":"K Meusemann","year":"2010","unstructured":"Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, K\u00fcck P, Ebersberger I, Walzl M, Pass G, Breuers S, Achter V, von Haeseler A, Burmester T, Hadrys H, W\u00e4gele JW, Misof B: A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol 2010, 27: 2451\u20132464. 10.1093\/molbev\/msq130","journal-title":"Mol Biol Evol"},{"key":"4347_CR4","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1163\/156854109X456862","volume":"11","author":"H van Megen","year":"2009","unstructured":"van Megen H, van den Elsen S, Holterman M, Karssen G, Mooyman P, Bongers T, Holovachov O, Bakker J, Helder J: A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences. Nematology 2009, 11: 927\u2013950. 10.1163\/156854109X456862","journal-title":"Nematology"},{"key":"4347_CR5","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1038\/nature02053","volume":"425","author":"A Rokas","year":"2003","unstructured":"Rokas A, Williams BL, King N, Carroll SB: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425: 798\u2013804. 10.1038\/nature02053","journal-title":"Nature"},{"key":"4347_CR6","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.tree.2006.10.002","volume":"22","author":"A de Queiroz","year":"2007","unstructured":"de Queiroz A, Gatesy J: The supermatrix approach to systematics. Trends in Ecology & Evolution 2007, 22: 34\u201341.","journal-title":"Trends in Ecology & Evolution"},{"key":"4347_CR7","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.jbi.2005.04.001","volume":"39","author":"JJ Wiens","year":"2006","unstructured":"Wiens JJ: Missing data and the design of phylogenetic analyses. J Biomed Inform 2006, 39: 34\u201342. 10.1016\/j.jbi.2005.04.001","journal-title":"J Biomed Inform"},{"key":"4347_CR8","doi-asserted-by":"publisher","first-page":"e7891","DOI":"10.1371\/journal.pone.0007891","volume":"4","author":"B Kolaczkowski","year":"2009","unstructured":"Kolaczkowski B, Thornton JW: Long-branch attraction bias and inconsistency in Bayesian phylogenetics. PLoS ONE 2009, 4: e7891. 10.1371\/journal.pone.0007891","journal-title":"PLoS ONE"},{"key":"4347_CR9","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.1093\/molbev\/msq097","volume":"27","author":"MP Nesnidal","year":"2010","unstructured":"Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B: Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol Biol Evol 2010, 27: 2095\u20132104. 10.1093\/molbev\/msq097","journal-title":"Mol Biol Evol"},{"key":"4347_CR10","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1093\/sysbio\/syp037","volume":"58","author":"NC Sheffield","year":"2009","unstructured":"Sheffield NC, Song H, Cameron SL, Whiting MF: Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Syst Biol 2009, 58: 381\u2013394. 10.1093\/sysbio\/syp037","journal-title":"Syst Biol"},{"issue":"Suppl 1","key":"4347_CR11","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2148-7-S1-S2","volume":"7","author":"B Roure","year":"2007","unstructured":"Roure B, Rodriguez-Ezpeleta N, Philippe H: SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol 2007, 7(Suppl 1):S2. 10.1186\/1471-2148-7-S1-S2","journal-title":"BMC Evol Biol"},{"key":"4347_CR12","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1126\/science.273.5275.569","volume":"273","author":"V Morell","year":"1996","unstructured":"Morell V: TreeBASE: The Roots of Phylogeny. Science 1996, 273: 569\u20130. 10.1126\/science.273.5275.569","journal-title":"Science"},{"key":"4347_CR13","doi-asserted-by":"publisher","first-page":"D5","DOI":"10.1093\/nar\/gkn741","volume":"37","author":"EW Sayers","year":"2009","unstructured":"Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, 37: D5\u201315. 10.1093\/nar\/gkn741","journal-title":"Nucleic Acids Res"},{"key":"4347_CR14","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/30.1.27","volume":"30","author":"Y Tateno","year":"2002","unstructured":"Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H, Gojobori T: DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Research 2002, 30: 27\u201330. 10.1093\/nar\/30.1.27","journal-title":"Nucleic Acids Research"},{"key":"4347_CR15","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1093\/nar\/30.1.21","volume":"30","author":"G Stoesser","year":"2002","unstructured":"Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Redaschi N, Stoehr P, Tuli MA, Tzouvara K, Vaughan R: The EMBL Nucleotide Sequence Database. Nucleic Acids Res 2002, 30: 21\u201326. 10.1093\/nar\/30.1.21","journal-title":"Nucleic Acids Res"},{"key":"4347_CR16","doi-asserted-by":"publisher","first-page":"D735","DOI":"10.1093\/nar\/gkm1005","volume":"36","author":"J Ruan","year":"2008","unstructured":"Ruan J, Li H, Chen Z, Coghlan A, Coin LJM, Guo Y, H\u00e9rich\u00e9 J, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R: TreeFam: 2008 Update. Nucleic Acids Res 2008, 36: D735\u2013740. 10.1093\/nar\/gkm1005","journal-title":"Nucleic Acids Res"},{"key":"4347_CR17","doi-asserted-by":"publisher","first-page":"D138","DOI":"10.1093\/nar\/gkh121","volume":"32","author":"A Bateman","year":"2004","unstructured":"Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res 2004, 32: D138\u2013141. 10.1093\/nar\/gkh121","journal-title":"Nucleic Acids Res"},{"key":"4347_CR18","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","volume":"23","author":"I Letunic","year":"2007","unstructured":"Letunic I, Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23: 127\u2013128. 10.1093\/bioinformatics\/btl529","journal-title":"Bioinformatics"},{"key":"4347_CR19","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1186\/1471-2105-10-219","volume":"10","author":"F Schreiber","year":"2009","unstructured":"Schreiber F, Pick K, Erpenbeck D, W\u00f6rheide G, Morgenstern B: OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. BMC Bioinformatics 2009, 10: 219. 10.1186\/1471-2105-10-219","journal-title":"BMC Bioinformatics"},{"key":"4347_CR20","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1186\/1471-2105-9-518","volume":"9","author":"ACJ Roth","year":"2008","unstructured":"Roth ACJ, Gonnet GH, Dessimoz C: Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics 2008, 9: 518. 10.1186\/1471-2105-9-518","journal-title":"BMC Bioinformatics"},{"key":"4347_CR21","doi-asserted-by":"publisher","first-page":"2096","DOI":"10.1093\/bioinformatics\/btn397","volume":"24","author":"RCG Holland","year":"2008","unstructured":"Holland RCG, Down TA, Pocock M, Prli\u0107 A, Huen D, James K, Foisy S, Dr\u00e4ger A, Yates A, Heuer M, Schreiber MJ: BioJava: an open-source framework for bioinformatics. Bioinformatics 2008, 24: 2096\u20132097. 10.1093\/bioinformatics\/btn397","journal-title":"Bioinformatics"},{"key":"4347_CR22","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"4347_CR23","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","volume":"85","author":"WR Pearson","year":"1988","unstructured":"Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85: 2444\u20132448. 10.1073\/pnas.85.8.2444","journal-title":"Proc Natl Acad Sci USA"},{"key":"4347_CR24","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1101\/gr.9.9.868","volume":"9","author":"X Huang","year":"1999","unstructured":"Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9: 868\u2013877. 10.1101\/gr.9.9.868","journal-title":"Genome Res"},{"key":"4347_CR25","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32: 1792\u20131797. 10.1093\/nar\/gkh340","journal-title":"Nucleic Acids Res"},{"key":"4347_CR26","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16: 276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"},{"key":"4347_CR27","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","volume":"25","author":"AM Waterhouse","year":"2009","unstructured":"Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ: Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25: 1189\u20131191. 10.1093\/bioinformatics\/btp033","journal-title":"Bioinformatics"},{"key":"4347_CR28","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22: 2688\u20132690. 10.1093\/bioinformatics\/btl446","journal-title":"Bioinformatics"},{"key":"4347_CR29","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","volume":"19","author":"F Ronquist","year":"2003","unstructured":"Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19: 1572\u20131574. 10.1093\/bioinformatics\/btg180","journal-title":"Bioinformatics"},{"key":"4347_CR30","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/1471-2148-7-214","volume":"7","author":"AJ Drummond","year":"2007","unstructured":"Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7: 214. 10.1186\/1471-2148-7-214","journal-title":"BMC Evol Biol"},{"key":"4347_CR31","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1093\/sysbio\/46.4.590","volume":"46","author":"DR Maddison","year":"1997","unstructured":"Maddison DR, Swofford DL, Maddison WP: NEXUS: an extensible file format for systematic information. Syst Biol 1997, 46: 590\u2013621. 10.1093\/sysbio\/46.4.590","journal-title":"Syst Biol"},{"key":"4347_CR32","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1186\/1471-2105-10-356","volume":"10","author":"M Han","year":"2009","unstructured":"Han M, Zmasek C: phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 2009, 10: 356. 10.1186\/1471-2105-10-356","journal-title":"BMC Bioinformatics"},{"key":"4347_CR33","doi-asserted-by":"publisher","first-page":"D492","DOI":"10.1093\/nar\/gkp858","volume":"38","author":"LY Geer","year":"2010","unstructured":"Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH: The NCBI BioSystems database. Nucleic Acids Res 2010, 38: D492\u2013496. 10.1093\/nar\/gkp858","journal-title":"Nucleic Acids Res"},{"key":"4347_CR34","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","volume":"22","author":"W Li","year":"2006","unstructured":"Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22: 1658\u20131659. 10.1093\/bioinformatics\/btl158","journal-title":"Bioinformatics"},{"key":"4347_CR35","doi-asserted-by":"publisher","first-page":"D427","DOI":"10.1093\/nar\/gkh018","volume":"32","author":"J Parkinson","year":"2004","unstructured":"Parkinson J, Whitton C, Schmid R, Thomson M, Blaxter M: NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acids Res 2004, 32: D427\u2013430. 10.1093\/nar\/gkh018","journal-title":"Nucleic Acids Res"},{"key":"4347_CR36","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/32160","volume":"392","author":"ML Blaxter","year":"1998","unstructured":"Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, Vanfleteren JR, Mackey LY, Dorris M, Frisse LM, Vida JT, Thomas WK: A molecular evolutionary framework for the phylum Nematoda. Nature 1998, 392: 71\u201375. 10.1038\/32160","journal-title":"Nature"},{"key":"4347_CR37","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1186\/1471-2105-7-536","volume":"7","author":"M Jones","year":"2006","unstructured":"Jones M, Blaxter M: TaxMan: a taxonomic database manager. BMC Bioinformatics 2006, 7: 536. 10.1186\/1471-2105-7-536","journal-title":"BMC Bioinformatics"},{"key":"4347_CR38","doi-asserted-by":"publisher","first-page":"1398","DOI":"10.1093\/bioinformatics\/bth101","volume":"20","author":"J Parkinson","year":"2004","unstructured":"Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M: PartiGene--constructing partial genomes. Bioinformatics 2004, 20: 1398\u20131404. 10.1093\/bioinformatics\/bth101","journal-title":"Bioinformatics"},{"key":"4347_CR39","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/1471-2148-10-210","volume":"10","author":"A Criscuolo","year":"2010","unstructured":"Criscuolo A, Gribaldo S: BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 2010, 10: 210. 10.1186\/1471-2148-10-210","journal-title":"BMC Evol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-30.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-30\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-30.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T09:16:47Z","timestamp":1548148607000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-30"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,1,24]]},"references-count":39,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4347"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-30","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,1,24]]},"article-number":"30"}}