@article{ankenbrand_bcgtree:_2016,
	title = {{bcgTree}: automatized phylogenetic tree building from bacterial core genomes},
	issn = {0831-2796},
	shorttitle = {{bcgTree}},
	url = {http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2015-0175},
	doi = {10.1139/gen-2015-0175},
	abstract = {The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate i...},
	urldate = {2016-05-13},
	journal = {Genome},
	author = {Ankenbrand, Markus J and Keller, Alexander},
	year = {2016},
}

{"_id":"cgXCvdniiGbA9kiB7","bibbaseid":"ankenbrand-keller-bcgtreeautomatizedphylogenetictreebuildingfrombacterialcoregenomes-2016","downloads":0,"creationDate":"2016-05-13T16:24:25.823Z","title":"bcgTree: automatized phylogenetic tree building from bacterial core genomes","author_short":["Ankenbrand, M. J","Keller, A."],"year":2016,"bibtype":"article","biburl":"https://api.zotero.org/users/2437131/collections/PIQAK8AJ/items?key=D2iCpfBnisKHHLPywQxwq6es&format=bibtex&limit=100","bibdata":{"bibtype":"article","type":"article","title":"bcgTree: automatized phylogenetic tree building from bacterial core genomes","issn":"0831-2796","shorttitle":"bcgTree","url":"http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2015-0175","doi":"10.1139/gen-2015-0175","abstract":"The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate i...","urldate":"2016-05-13","journal":"Genome","author":[{"propositions":[],"lastnames":["Ankenbrand"],"firstnames":["Markus","J"],"suffixes":[]},{"propositions":[],"lastnames":["Keller"],"firstnames":["Alexander"],"suffixes":[]}],"year":"2016","bibtex":"@article{ankenbrand_bcgtree:_2016,\n\ttitle = {{bcgTree}: automatized phylogenetic tree building from bacterial core genomes},\n\tissn = {0831-2796},\n\tshorttitle = {{bcgTree}},\n\turl = {http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2015-0175},\n\tdoi = {10.1139/gen-2015-0175},\n\tabstract = {The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate i...},\n\turldate = {2016-05-13},\n\tjournal = {Genome},\n\tauthor = {Ankenbrand, Markus J and Keller, Alexander},\n\tyear = {2016},\n}\n\n","author_short":["Ankenbrand, M. J","Keller, A."],"key":"ankenbrand_bcgtree:_2016","id":"ankenbrand_bcgtree:_2016","bibbaseid":"ankenbrand-keller-bcgtreeautomatizedphylogenetictreebuildingfrombacterialcoregenomes-2016","role":"author","urls":{"Paper":"http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2015-0175"},"metadata":{"authorlinks":{}}},"search_terms":["bcgtree","automatized","phylogenetic","tree","building","bacterial","core","genomes","ankenbrand","keller"],"keywords":[],"authorIDs":["5534ac016069983d700000b2","5df5c63864d1d0df01000074","5e1d481fe32442de0100002e","5e44d387ab9cedde0100001a","CvkAZSSJ2nRgJtS64","hE34ZmsogLHxHPbjf","onkpeKB7DAGQygP4L"],"dataSources":["H9HNT846ntJhBgngg"]}