0000000001320698

AUTHOR

Kasey K. Pham

showing 2 related works from this author

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

2016

Pham, Kasey K. [et al.]

0106 biological sciences0301 basic medicineBiodiversityPlant ScienceComputational biologyBiology010603 evolutionary biology01 natural sciencesSet (abstract data type)03 medical and health sciencesBotanyDNA databaseGeneticsSupermatrixEcology Evolution Behavior and SystematicsPhylogenetic treePhylogenetic workflowTaxon disparity index (TDI)030104 developmental biologyWorkflowCarexGenBankIdentity (object-oriented programming)CyperaceaeSupermatrixSpecimen-level data
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Data from: Specimens at the center: an informatics workflow and toolkit for specimen-level analysis of public DNA database data

2017

Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been…

medicine and health caretaxon disparity indexCarexphylogenetic workflowMedicinespecimen-level dataCyperaceaeSupermatrixLife sciences
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