Selected publications featuring Geneious

1. The mitochondrial genome of Colossendeis megalonyx supports a basal position of Colossendeidae within the Pycnogonida
   Lars Dietz, Christoph Mayer Claudia P. Arango , Florian Leese
   Molecular Phylogenetics and Evolution, 58 (2011) 553–558
   ...454 data processing was performed with Geneious version 5.0.3 (Drummond et al., 2009)...
2. Identification of species by multiplex analysis of variable-length sequences
   Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim, A.
   Nucleic Acids Research 2010. 38 (22): e203
   http://nar.oxfordjournals.org/content/38/22/e203
3. Genetic Analysis of a Novel Xylella fastidiosa Subspecies Found in the Southwestern United States
   Jennifer J. Randall, Natalie P. Goldberg, John D. Kemp, Maxim Radionenko, Jason M. French, Mary W. Olsen, and Stephen F. Hanson
   Appl. Envir. Microbiol., Sep 2009; 75: 5631 – 5638.
   ... ...sequence alignments were generated by using Geneious Pro v4.0.4 (8). Maximum-likelihood trees...alignments and phylogenetic trees using Geneious Pro v4.0.4. The maximum-likelihood method...A. Wilson, and S. Stones-Havas. 2006. Geneious, v2.5. Biomatters, Ltd., Auckland, New... ...
4. Virus-Induced Gene Silencing in the Culinary Ginger (Zingiber officinale): An Effective Mechanism for Down-Regulating Gene Expression in Tropical Monocots
   Tanya Renner, Jennifer Bragg, Heather E. Driscoll, Juliana Cho, Andrew O. Jackson, and Chelsea D. Specht
   Mol Plant, Sep 2009; 2: 1084 – 1094.
   ... ...identity as determined by the program Geneious v3.7 (Drummond et al., 2007; available at www.geneious.com/). The nucleotide sequence for the...Stones-Havas S, Thierer T, Wilson A. Geneious v3.7. (2007). Fu D , Uauy C, Blechl... ...
5. Phylogenetic distributions of British birds of conservation concern
   Gavin H Thomas
   Proc R Soc B, Sep 2008; 275: 2077 – 2083.
   ... ...former breeders (Dudley et al. 2006). I used Geneious v. 2.0 (Drummond et al. 2006b ) to search...Thierer, T., Ashton, B. Wilson, A. 2006b Geneious v. 2.0. Available from http://www.geneious.com/ . Dudley, S.P , M Gee, C Kehoe... ...
6. Isolation of Fungal Cellobiohydrolase I Genes from Sporocarps and Forest Soils by PCR
   Ivan P. Edwards, Rima A. Upchurch, and Donald R. Zak
   Appl. Envir. Microbiol, Jun 2008; 74: 3481 – 3489.
   ... ...aligned by using the ClustalX module within Geneious Pro 3.0.5 (Biomatters Ltd.) and examined...BioEdit, and contigs were constructed in Geneious 3.0.5. For the sequences derived from...matches, with the ClustalX module in Geneious Pro 3.0.5. The alignment was checked... ...
7. Reproductive compensation favours male-killing Wolbachia in a live-bearing host
   Julie L. Koop, David W. Zeh, Melvin M. Bonilla, and Jeanne A. Zeh
   Proc R Soc B, Nov 2009; 276: 4021 – 4028.
   ... ...sequences were assembled from forward and reverse sequences in Geneious Pro 4.5 (Biomatters Ltd). For both the wCsc1 and wCsc2 strains...included in the phylogenetic analyses. Sequences were aligned in Geneious with ClustalW (Larkin et al. 2007), and phylogenetic analyses... ...
8. Sensitive Multiplex Real-Time Reverse Transcription-PCR Assay for the Detection of Human and Animal Noroviruses in Clinical and Environmental Samples
   Sandro Wolf, Wendy M. Williamson, Joanne Hewitt, Malet Rivera-Aban, Susan Lin, Andrew Ball, Paula Scholes, and Gail E. Greening
   Appl. Envir. Microbiol., Sep 2007; 73: 5464 – 5470.
   ... ...were aligned using ClustalW, version 1.83, implemented in Geneious, version 2.0.4 (Biomatters Ltd.) (Table 1). The alignment was...Sequences were aligned using ClustalW, version 1.83, implemented in Geneious, version, 2.5.2. Phylogenetic analysis was performed using... ...
9. Genotypic Comparison of Invasive Neisseria meningitidis Serogroup Y Isolates from the United States, South Africa, and Israel, Isolated from 1999 through 2002
   Anne M. Whitney, Garry B. Coulson, Anne von Gottberg, Colin Block, Nathan Keller, Leonard W. Mayer, Nancy E. Messonnier, and Keith P. Klugman
   J. Clin. Microbiol., Sep 2009; 47: 2787 – 2793.
   ... ...Diego, CA). Phylogenetic analysis was performed by using Geneious (A. J. Drummond, B. Ashton, M. Cheung, J. Heled, M. Kearse, R. Moir, S. Stones-Havas, T. Thierer, and A. Wilson, Geneious v3.8.). RESULTS Three hundred NmY isolates collected... ...
10. A single nucleotide polymorphism determines protein isoform production of the human c-FLIP protein
    Nana Ueffing, Kusum K. Singh, Andrea Christians, Christoph Thorns, Alfred C. Feller, Florian Nagl, Falko Fend, Sebastian Heikaus, Alexander Marx, Rainer B. Zotz, Joachim Brade, Wolfgang A. Schulz, Klaus Schulze-Osthoff, Ingo Schmitz, and Christian Schwerk
    Blood, Jul 2009; 114: 572 – 579.
    ... ...mammals. (A) Sequence alignment of mammalian c-FLIPS and c-FLIPR proteins. Alignments were performed using Geneious software ( http://www.geneious.com ). Sequences are shown in single-letter amino acid code. (B) Analysis of c-FLIP genomic sequences... ...
11. From the Cover: Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes
    Adam C. Martiny, Satish Kathuria, and Paul M. Berube
    PNAS, Jun 2009; 106: 10787 – 10792.
    ... ...sequences from GOS and Cyanobacteria genomes using the software Geneious (Biomatters) and carefully curated the alignments manually...Prochlorococcus sequences. The scaffold in Fig. 1 B is assembled using Geneious and manually curated, and is based on 269 sequences from GOS... ...
12. Historical Divergence and Gene Flow in the Genus Zea
    Jeffrey Ross-Ibarra, Maud Tenaillon, and Brandon S. Gaut
    Genetics, Apr 2009; 181: 1399 – 1413.
    ... ...analysis: Sequences were initially aligned using the software Geneious (Biomatters) and then manually adjusted. Twelve of these loci...using a combination of the ORF-finding software at NCBI and in Geneious and using blastn searches of mRNA databases in GenBank. Final... ...
13. Sterols in a unicellular relative of the metazoans
    Robin B. Kodner, Roger E. Summons, Ann Pearson, Nicole King, and Andrew H. Knoll
    PNAS, Jul 2008; 105: 9897 – 9902.
    ... ...proteins and by phylogenetic tree constructions. Protein alignments for phylogenetic analysis were made with Geneious 2.0.1 ( www.geneious.com ) with Blosum 62 cost matrix, free end gaps, and two refinement iterations. Alignments were realigned... ...
14. Molecular Characterization of Ciliate Diversity in Stream Biofilms
    Andrew Dopheide, Gavin Lear, Rebecca Stott, and Gillian Lewis
    Appl. Envir. Microbiol., Mar 2008; 74: 1740 – 1747.
    ... ...stream biofilms were retrieved from GenBank, aligned using Geneious 2.0.1 (Biomatters Ltd., NZ; developed by A. J. Drummond, M...match the same GenBank sequence were compared by alignment in Geneious 2.0.1, and those sharing less than 97 nucleotide identity were... ...
15. Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa
    Alex R. Hall, Victoria F. Griffiths, R. Craig MacLean, and Nick Colegrave
    Proc R Soc B, Nov 2009; 10.1098/rspb.2009.1630.
    ... ...EDTA precipitation. Sequences were then edited and aligned against the wild-type PA01 rpoB sequence from GenBank (NCBI) using Geneious Pro 4.5.5. (Biomatters Ltd). Control samples showed that the obtained PA01 sequence was as expected, and the H531R and H531Y... ...
16. Saprolegniaceae identified on amphibian eggs throughout the Pacific Northwest, USA, by internal transcribed spacer sequences and phylogenetic analysis
    Jill E. Petrisko, Christopher A. Pearl, David S. Pilliod, Peter P. Sheridan, Charles F. Williams, Charles R. Peterson, and R. Bruce Bury
    Mycologia, Mar 2008; 100: 171 – 180.
    ... ...sequence homology (Altschul et al 1990). To see the phylogenetic relationships among our Saprolegniaceae sequences, we used Geneious Pro (version 2.5.2) to produce a multiple global alignment of 88 sequences. The sequences in our phylogeny included: (i) all... ...
17. Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens
    Konrad Trülzsch, Béatrice Grabein, Peter Schumann, Alexander Mellmann, Uladzimir Antonenka, Jürgen Heesemann, and Karsten Becker
    Int J Syst Evol Microbiol, Jul 2007; 57: 1543 – 1548.
    ... ...tree by the neighbour-joining method and bootstrapping analysis based on 1000 resamplings were performed using the software geneious 2.5.4 Biomatters. Partial RNA polymerase B rpoB sequencing was performed as reported previously Mellmann et al., 2006. For... ...
18. Microbial community composition of the crop and ceca contents of laying hens fed diets supplemented with Chlorella vulgaris
    P. Janczyk, B. Halle, and W. B. Souffrant
    Poult. Sci., Nov 2009; 88: 2324 – 2332.
    ... ...et al., 2007b). The retrieved forward and reverse sequences were aligned and a consensus sequence was established using the Geneious software version 4.6.2 (Biomatters Ltd., Auckland, New Zealand). The consensus sequences were further trimmed applying the... ...
19. Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata
    Solomon Stonebloom, Tessa Burch-Smith, Insoon Kim, David Meinke, Michael Mindrinos, and Patricia Zambryski
    PNAS, Oct 2009; 106: 17229 – 17234.
    ... ...dopsis thaliana were retrieved from GenBank. Sequences were aligned using the MUSCLE algorithm with the default settings in Geneious (Biomatters). This alignment was used to generate a maximum parsimony tree with bootstrap values with PAUP* 4.0 (Sinauer Associates... ...
20. Surface Colonization by Marine Roseobacters: Integrating Genotype and Phenotype
    Rachael N. Slightom and Alison Buchan
    Appl. Envir. Microbiol., Oct 2009; 75: 6027 – 6037.
    ... ...in-house annotation pipeline. Scaffolds were downloaded and subjected to homology searches and additional analyses locally using Geneious 3.0.6 (Biomatters Ltd., Auckland, New Zealand). Of these genomes, five have been closed (Jannaschia sp. strain CCS1, Roseobacter... ...
21. Evolutionarily Conserved Regulatory Motifs in the Promoter of the Arabidopsis Clock Gene LATE ELONGATED HYPOCOTYL
    Mark Spensley, Jae-Yean Kim, Emma Picot, John Reid, Sascha Ott, Chris Helliwell, and Isabelle A. Carré
    PLANT CELL, Sep 2009; 21: 2606 – 2623.
    ... ...position in the promoter is termed conservation profile in the context of this work. Sequence alignments were generated using Geneious v4.0. ChIP ChIP analysis for FLC binding was performed essentially as described (Helliwell et al., 2006). Briefly, 1 g... ...
22. Sexual Development in Lucilia cuprina (Diptera, Calliphoridae) Is Controlled by the Transformer Gene
    Carolina Concha and Maxwell J. Scott
    Genetics, Jul 2009; 182: 785 – 798.
    ... ...alignments was performed using BOX SHADE. Phylogenetic analysis was carried out using a basic neighbor-joining algorithm in the Geneious software package and FigTree v1.1.1 was used to draw the tree. The putative TRA-TRA2 binding sites were identified in Lctra... ...
23. Autoprocessing of the Escherichia coli AIDA-I Autotransporter: A NEW MECHANISM INVOLVING ACIDIC RESIDUES IN THE JUNCTION REGION
    Marie-Ève Charbonneau, Julie Janvore, and Michael Mourez
    J. Biol. Chem., Jun 2009; 284: 17340 – 17351.
    ... ...generated using the PyMol software (Delano Scientific LLC). Sequence alignment was performed using the BLOSUM 62 matrix, with the Geneious Pro 4.0.2 software (Biomatters Ltd.). RESULTS A Purified Mutant of AIDA-I Undergoes Self-cleavage in Vitro... ...
24. Cloning and functional expression of the first eukaryotic Na+–tryptophan symporter, AgNAT6
    Ella A. Meleshkevitch, Marvin Robinson, Lyudmila B. Popova, Melissa M. Miller, William R. Harvey, and Dmitri Y. Boudko
    J. Exp. Biol., May 2009; 212: 1559 – 1567.
    ... ...this figure), which is supported by structural alignment, and substrate docking (not shown). The alignment was generated by Geneious Pro 4.5 software (Biomatters, Auckland, New Zealand) with a minor manual improvement. Increasing background intensity indicates... ...
25. Identification of the Small Protein Rich in Arginine and Glycine (SRAG): A NEWLY IDENTIFIED NUCLEOLAR PROTEIN THAT CAN REGULATE CELL PROLIFERATION
    Alfred J. Zullo, Monia Michaud, Weiping Zhang, and Michael J. Grusby
    J. Biol. Chem., May 2009; 284: 12504 – 12511.
    ... ...SRAG/C1orf77 (NP_056422) were obtained from NCBI. The alignment of human SRAG, nucleolin, and fibrillarin was performed using Geneious Basic v3.85 using a Blosum62 matrix. The multiple organism alignment was prepared similarly using the following additional... ...
26. Instability of Superoxide Dismutase 1 of Drosophila in Mutants Deficient for Its Cognate Copper Chaperone
    Kim Kirby, Laran T. Jensen, Janet Binnington, Arthur J. Hilliker, Janella Ulloa, Valeria C. Culotta, and John P. Phillips
    J. Biol. Chem., Dec 2008; 283: 35393 – 35401.
    ... ...proteins from fungi, plants, and animals. Sequences were obtained from the GenBank database. Alignments were performed with Geneious (version 3.0.6). Ccs Deletion Mutation-A loss of function mutation of Ccs (Ccsn 29 E ), generated by an apparent imprecise... ...
27. Multiple Virus Lineages Sharing Recent Common Ancestry Were Associated with a Large Rift Valley Fever Outbreak among Livestock in Kenya during 2006-2007
    Brian H. Bird, Jane W. K. Githinji, Joseph M. Macharia, Jacqueline L. Kasiiti, Rees M. Muriithi, Stephen G. Gacheru, Joseph O. Musaa, Jonathan S. Towner, Serena A. Reeder, Jennifer B. Oliver, Thomas L. Stevens, Bobbie R. Erickson, Laura T. Morgan, Marina L. Khristova, Amy L. Hartman, James A. Comer, Pierre E. Rollin, Thomas G. Ksiazek, and Stuart T. Nichol
    J. Virol., Nov 2008; 82: 11152 – 11166.
    ... ...resulting in an average sixfold redundancy at each base position. Phylogenetic analyses. Sequence datasets were analyzed using Geneious (BioMatters), Seaview (21), the MAFFT alignment program (24), and the PAUP program, version 4.0b10 (Sinauer Associates, Inc... ...