Brant C Faircloth

Brant C Faircloth

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Brant C Faircloth

Publications by authors named "Brant C Faircloth"

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Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest.

Mol Phylogenet Evol 2019 12 17;141:106627. Epub 2019 Sep 17.

Moore Laboratory of Zoology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA.

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http://dx.doi.org/10.1016/j.ympev.2019.106627DOI Listing
December 2019

A Highly Contiguous Reference Genome for Northern Bobwhite ().

G3 (Bethesda) 2019 12 3;9(12):3929-3932. Epub 2019 Dec 3.

Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana,

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http://dx.doi.org/10.1534/g3.119.400609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893191PMC
December 2019

Correction: Cultivation and genomics of the first freshwater SAR11 (LD12) isolate.

ISME J 2019 Dec 13. Epub 2019 Dec 13.

Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.

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http://dx.doi.org/10.1038/s41396-019-0569-7DOI Listing
December 2019

What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?

Mol Phylogenet Evol 2019 01 12;130:132-142. Epub 2018 Oct 12.

Department of Biology, University of Florida, Gainesville, FL 32611, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183019
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http://dx.doi.org/10.1016/j.ympev.2018.10.008DOI Listing
January 2019

Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources.

Mol Phylogenet Evol 2019 01 22;130:297-303. Epub 2018 Oct 22.

Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.

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http://dx.doi.org/10.1016/j.ympev.2018.10.026DOI Listing
January 2019

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird.

Mol Ecol 2018 12 21;27(24):5137-5153. Epub 2018 Dec 21.

National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain.

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http://dx.doi.org/10.1111/mec.14946DOI Listing
December 2018

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event.

PeerJ 2018 5;6:e5735. Epub 2018 Oct 5.

Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.

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https://peerj.com/articles/5735
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http://dx.doi.org/10.7717/peerj.5735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174879PMC
October 2018

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate.

ISME J 2018 06 29;12(7):1846-1860. Epub 2018 Mar 29.

Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.

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http://dx.doi.org/10.1038/s41396-018-0092-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018831PMC
June 2018

Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary.

Nat Ecol Evol 2018 04 12;2(4):688-696. Epub 2018 Mar 12.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1038/s41559-018-0494-6DOI Listing
April 2018

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes.

Syst Biol 2017 Nov;66(6):881-895

Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/sysbio/syx038DOI Listing
November 2017

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).

PLoS One 2013 18;8(6):e65923. Epub 2013 Jun 18.

Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065923PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688804PMC
October 2017

Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit.

Mol Phylogenet Evol 2017 09 1;114:40-48. Epub 2017 Jun 1.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1016/j.ympev.2017.05.027DOI Listing
September 2017

Phylogenetic relationships of diurnal, phytotelm-breeding Melanophryniscus (Anura: Bufonidae) based on mitogenomic data.

Gene 2017 Sep 15;628:194-199. Epub 2017 Jul 15.

Moore Laboratory of Zoology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA.

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http://dx.doi.org/10.1016/j.gene.2017.07.048DOI Listing
September 2017

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements.

Genome Biol Evol 2017 09;9(9):2308-2321

Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge.

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http://dx.doi.org/10.1093/gbe/evx168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604124PMC
September 2017

Polyandry enhances offspring viability with survival costs to mothers only when mating exclusively with virgin males in .

Ecol Evol 2017 09 14;7(18):7515-7526. Epub 2017 Aug 14.

Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles CA USA.

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http://dx.doi.org/10.1002/ece3.3152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5606902PMC
September 2017

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida.

Mol Ecol Resour 2017 Jul 19;17(4):812-823. Epub 2016 Nov 19.

Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.

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http://dx.doi.org/10.1111/1755-0998.12621DOI Listing
July 2017

Phylogenomic Insights into the Evolution of Stinging Wasps and the Origins of Ants and Bees.

Curr Biol 2017 Apr;27(7):1019-1025

Department of Entomology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, 10(th) Street and Constitution Avenue NW, Washington, DC 20560, USA.

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http://dx.doi.org/10.1016/j.cub.2017.03.027DOI Listing
April 2017

Dry habitats were crucibles of domestication in the evolution of agriculture in ants.

Proc Biol Sci 2017 Apr;284(1852)

Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA

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http://dx.doi.org/10.1098/rspb.2017.0095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5394666PMC
April 2017

Hidden histories of gene flow in highland birds revealed with genomic markers.

Mol Ecol 2016 10 12;25(20):5144-5157. Epub 2016 Sep 12.

Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA.

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http://dx.doi.org/10.1111/mec.13813DOI Listing
October 2016

Sequence capture of ultraconserved elements from bird museum specimens.

Mol Ecol Resour 2016 Sep 24;16(5):1189-203. Epub 2015 Oct 24.

Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.

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http://dx.doi.org/10.1111/1755-0998.12466DOI Listing
September 2016

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Syst Biol 2016 Sep 10;65(5):910-24. Epub 2016 Jun 10.

Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1093/sysbio/syw036DOI Listing
September 2016

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data.

Mol Ecol Resour 2016 Sep;16(5):1264-78

Department of Genetics, University of Georgia, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1111/1755-0998.12566DOI Listing
September 2016

Capturing Darwin's dream.

Mol Ecol Resour 2016 Sep;16(5):1051-8

Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA.

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http://dx.doi.org/10.1111/1755-0998.12574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5318190PMC
September 2016

Tectonic collision and uplift of Wallacea triggered the global songbird radiation.

Nat Commun 2016 08 30;7:12709. Epub 2016 Aug 30.

Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1038/ncomms12709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013600PMC
August 2016

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods.

Syst Biol 2016 Jul 10;65(4):612-27. Epub 2016 Feb 10.

Department of Biology, University of Florida, Gainesville, FL; Genetics Institute, University of Florida, Gainesville, FL.

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http://dx.doi.org/10.1093/sysbio/syw014DOI Listing
July 2016

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).

Mol Biol Evol 2016 Apr 29;33(4):1110-25. Epub 2015 Dec 29.

Department of Biology, University of Florida.

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http://dx.doi.org/10.1093/molbev/msv347DOI Listing
April 2016

PHYLUCE is a software package for the analysis of conserved genomic loci.

Bioinformatics 2016 03 2;32(5):786-8. Epub 2015 Nov 2.

Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv646DOI Listing
March 2016

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

Ecol Lett 2015 Dec 16;18(12):1397-405. Epub 2015 Oct 16.

Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.

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http://dx.doi.org/10.1111/ele.12536DOI Listing
December 2015

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.

Mol Phylogenet Evol 2015 Nov 12;92:140-6. Epub 2015 Jun 12.

Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2015.05.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583375PMC
November 2015

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.

Mol Ecol Resour 2015 May 29;15(3):489-501. Epub 2014 Sep 29.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.

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http://dx.doi.org/10.1111/1755-0998.12328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407909PMC
May 2015

A phylogenomic analysis of turtles.

Mol Phylogenet Evol 2015 Feb 4;83:250-7. Epub 2014 Nov 4.

Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.

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http://dx.doi.org/10.1016/j.ympev.2014.10.021DOI Listing
February 2015

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

The drivers of tropical speciation.

Nature 2014 Nov 10;515(7527):406-9. Epub 2014 Sep 10.

1] Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA [2] Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA [3].

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http://dx.doi.org/10.1038/nature13687DOI Listing
November 2014

Incongruence among different mitochondrial regions: a case study using complete mitogenomes.

Mol Phylogenet Evol 2014 Sep 12;78:314-23. Epub 2014 Jun 12.

Department of Biology, University of Florida, Gainesville, FL, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2014.06.003DOI Listing
September 2014

Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales.

Syst Biol 2014 Jan 10;63(1):83-95. Epub 2013 Sep 10.

Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; and Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/sysbio/syt061DOI Listing
January 2014

Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels.

PLoS One 2012 10;7(8):e42543. Epub 2012 Aug 10.

Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042543PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416851PMC
March 2013

Next-generation phylogenetics takes root.

Mol Ecol 2013 Jan;22(1):19-20

Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA.

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http://dx.doi.org/10.1111/mec.12050DOI Listing
January 2013

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

Syst Biol 2012 Oct 9;61(5):717-26. Epub 2012 Jan 9.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/sysbio/sys004DOI Listing
October 2012

Primer3--new capabilities and interfaces.

Nucleic Acids Res 2012 Aug 22;40(15):e115. Epub 2012 Jun 22.

Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany.

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http://dx.doi.org/10.1093/nar/gks596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584PMC
August 2012

Translocation to a fragmented landscape: survival, movement, and site fidelity of Northern Bobwhites.

Ecol Appl 2010 Jun;20(4):1040-52

D. B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1890/09-1106.1DOI Listing
June 2010

Tetranucleotide microsatellite loci from the black bear (Ursus americanus).

Mol Ecol Resour 2009 Jan 10;9(1):288-91. Epub 2008 Nov 10.

D. B. Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA 30602, USA, USGS, Georgia Cooperative Fish and Wildlife Research Unit, D.B. Warnell School of Forestry and Natural Resources, Athens, GA 30602, USA.

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http://dx.doi.org/10.1111/j.1755-0998.2008.02234.xDOI Listing
January 2009

Microsatellite markers for eastern hemlock (Tsuga canadensis).

Mol Ecol Resour 2008 Nov 3;8(6):1354-6. Epub 2008 Sep 3.

D. B. Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA 30602, USA, Southern Research Station, Southern Institute of Forest Genetics, USDA Forest Service, Saucier, MS 39574, USA.

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http://dx.doi.org/10.1111/j.1755-0998.2008.02274.xDOI Listing
November 2008

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.

Mol Ecol Resour 2008 Jan;8(1):92-4

D. B. Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1111/j.1471-8286.2007.01884.xDOI Listing
January 2008