{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T15:04:06Z","timestamp":1722697446097},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Pairwise comparisons of disagreement in phylogenetic datasets offer a powerful tool for isolating historical incongruence for closer analysis. Statistically significant phylogenetic character incongruence may reflect important differences in evolutionary history, such as horizontal gene transfer. Such testing can also be used to specify possible combinations of datasets for further phylogenetic analysis. The process of comparing multiple datasets can be very time consuming, and it is sometimes unclear how to combine data partitions given the observed patterns of incongruence. Here we present an application that automates the process of making pairwise comparisons between large numbers of phylogenetic datasets using the Incongruence Length Difference (ILD) test. The application also implements strategies for data combination based on the patterns of incongruence observed in pairwise comparisons.<\/jats:p>\n               <jats:p>Availability: The application is freely available as a Perl script that interacts with the command-line version of PAUP*.<\/jats:p>\n               <jats:p>Contact: \u00a0sarkar@amnh.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti744","type":"journal-article","created":{"date-parts":[[2005,11,3]],"date-time":"2005-11-03T01:13:48Z","timestamp":1130980428000},"page":"4423-4424","source":"Crossref","is-referenced-by-count":16,"title":["mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests"],"prefix":"10.1093","volume":"21","author":[{"given":"Paul J.","family":"Planet","sequence":"first","affiliation":[{"name":"Division of Invertebrate Zoology, American Museum of Natural History 1 \u00a0 1 \u00a0 \u00a0 New York, NY, USA"}]},{"given":"Indra Neil","family":"Sarkar","sequence":"additional","affiliation":[{"name":"Division of Invertebrate Zoology, American Museum of Natural History 1 \u00a0 1 \u00a0 \u00a0 New York, NY, USA"},{"name":"Division of Library Services, American Museum of Natural History 2 \u00a0 2 \u00a0 \u00a0 New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2005,11,2]]},"reference":[{"key":"2023061007325800400_b1","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1093\/sysbio\/46.4.654","article-title":"Multiple sources of character information and the phylogeny of Hawaiian drosophilids","volume":"46","author":"Baker","year":"1997","journal-title":"Syst. Biol."},{"key":"2023061007325800400_b2","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1080\/10635150290102302","article-title":"The utility of the incongruence length difference test","volume":"51","author":"Barker","year":"2002","journal-title":"Syst. Biol."},{"key":"2023061007325800400_b3","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/S1055-7903(02)00222-1","article-title":"Detection of recombination among Salmonella enterica strains using the incongruence length difference test","volume":"24","author":"Brown","year":"2002","journal-title":"Mol. Phylogenet. Evol."},{"key":"2023061007325800400_b4","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1093\/oxfordjournals.molbev.a004098","article-title":"When does the incongruence length difference test fail?","volume":"19","author":"Darlu","year":"2002","journal-title":"Mol. Biol. Evol."},{"key":"2023061007325800400_b5","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1006\/mpev.2000.0845","article-title":"Noise and incongruence: interpreting results of the incongruence length difference test","volume":"17","author":"Dolphin","year":"2000","journal-title":"Mol. Phylogenet. Evol."},{"key":"2023061007325800400_b6","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1080\/106351502753475853","article-title":"Increased congruence does not necessarily indicate increased phylogenetic accuracy\u2014the behavior of the incongruence length difference test in mixed-model analyses","volume":"51","author":"Dowton","year":"2002","journal-title":"Syst. Biol."},{"key":"2023061007325800400_b7","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/S1055-7903(03)00181-7","article-title":"Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study","volume":"30","author":"Escobar-Paramo","year":"2004","journal-title":"Mol. Phylogenet. Evol."},{"key":"2023061007325800400_b8","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1111\/j.1096-0031.1994.tb00181.x","article-title":"Testing the Significance of Incongruence","volume":"10","author":"Farris","year":"1994","journal-title":"Cladistics"},{"key":"2023061007325800400_b9","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1080\/10635150490264752","article-title":"Congruence Versus Phylogenetic Accuracy: Revisiting the Incongruence Length Difference Test","volume":"53","author":"Hipp","year":"2004","journal-title":"Syst. Biol."},{"key":"2023061007325800400_b10","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1093\/oxfordjournals.molbev.a025895","article-title":"Escherichia coli molecular phylogeny using the incongruence length difference test","volume":"15","author":"Lecointre","year":"1998","journal-title":"Mol. Biol. Evol."},{"key":"2023061007325800400_b11","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1111\/j.1463-6409.2005.00168.x","article-title":"Total Evidence require exclusion of phylogenetically misleading data","volume":"34","author":"Lecointre","year":"2005","journal-title":"Zoologica Scripta"},{"key":"2023061007325800400_b12","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/ng1154","article-title":"The Widespread Colonization Island of Actinobacillus actinomycetemcomitans","volume":"34","author":"Planet","year":"2003","journal-title":"Nat. Genet."},{"key":"2023061007325800400_b13","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1080\/106351501300318003","article-title":"Failure of the ILD to determine data combinability for slow loris phylogeny","volume":"50","author":"Yoder","year":"2001","journal-title":"Syst. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/24\/4423\/50566271\/bioinformatics_21_24_4423.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/24\/4423\/50566271\/bioinformatics_21_24_4423.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T07:33:27Z","timestamp":1686382407000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/24\/4423\/180584"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,11,2]]},"references-count":13,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2005,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti744","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,12,15]]},"published":{"date-parts":[[2005,11,2]]}}}