Ruiz-Ponte C, Cilia V, Lambert C, Nicolas JL. Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus. Int J Syst Bacteriol 1998; 48:537–542. PubMed http://dx.doi.org/10.1099/00207713-48-2-537
Article
CAS
PubMed
Google Scholar
Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola. Int J Syst Evol Microbiol 2006; 56:1293–1304. PubMed http://dx.doi.org/10.1099/ijs.0.63724-0
Article
CAS
PubMed
Google Scholar
Buddruhs N, Pradella S, Göker M, Päuker O, Pukall R, Spröer C, Schumann P, Petersen J, Brinkhoff T. Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395. Int J Syst Evol Microbiol 2013; 63:4340–4349. PubMed http://dx.doi.org/10.1099/ijs.0.053900-0
Article
CAS
PubMed
Google Scholar
Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M, et al. Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME J 2012; 6:2229–2244. PubMed http://dx.doi.org/10.1038/ismej.2012.62
Article
PubMed Central
CAS
PubMed
Google Scholar
Porsby CH, Nielsen KF, Gram L. Phaeobacter and Ruegeria species of the Roseobacter clade colonize separate niches in a Danish Turbot (Scophthalmus maximus)-rearing farm and antagonize Vibrio anguillarum under different growth conditions. Appl Environ Microbiol 2008; 74:7356–7364. PubMed http://dx.doi.org/10.1128/AEM.01738-08
Article
PubMed Central
CAS
PubMed
Google Scholar
Fernandes N, Case RJ, Longford SR, Seyedsayamdost MR, Steinberg PD, Kjelleberg S, Thomas T. Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra. PLoS ONE 2011; 6:e27387. PubMed http://dx.doi.org/10.1371/journal.pone.0027387
Article
PubMed Central
CAS
PubMed
Google Scholar
Seyedsayamdost MR, Case RJ, Kolter R, Clardy J. The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis. Nat Chem 2011; 3:331–335. PubMed http://dx.doi.org/10.1038/nchem.1002
Article
PubMed Central
CAS
PubMed
Google Scholar
Seyedsayamdost MR, Carr G, Kolter R, Clardy J. Roseobacticides: small molecule modulators of an algal-bacterial symbiosis. J Am Chem Soc 2011; 133:18343–18349. PubMed http://dx.doi.org/10.1021/ja207172s
Article
PubMed Central
CAS
PubMed
Google Scholar
Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, et al. Complete genome sequence of Isosphaera pallida type strain (IS1BT). Stand Genomic Sci 2011; 4:63–71. PubMed http://dx.doi.org/10.4056/sigs.1533840
Article
PubMed Central
PubMed
Google Scholar
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed http://dx.doi.org/10.1093/nar/gkp848
Article
PubMed Central
CAS
PubMed
Google Scholar
Freese HM, Dalingault H, Petersen J, Pradella S, Davenport K, Teshima H, Chen A, Pati A, Ivanova N, Goodwin LA, et al. Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T. Stand Genomic Sci 2013; 8:450–464. PubMed http://dx.doi.org/10.4056/sigs.383362
Article
PubMed Central
PubMed
Google Scholar
Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, et al. Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing member of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci 2013; 9:142–159. PubMed http://dx.doi.org/10.4056/sigs.4287962
Article
PubMed Central
PubMed
Google Scholar
Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, et al. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 2013; 8:403–419. PubMed http://dx.doi.org/10.4056/sigs.3927626
Article
PubMed Central
PubMed
Google Scholar
Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, et al. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium iso-lated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 2013; 9:142–159. PubMed http://dx.doi.org/10.4056/sigs.4287962
Article
PubMed Central
PubMed
Google Scholar
Riedel T, Teshima H, Petersen J, Fiebig A, Davenport K, Daligault H, Erkkila T, Gu W, Munk C, Xu Y, et al. Genome sequence of the Leisingera aquimarina type strain DSM 24565T, a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci 2013; 8:389–402. PubMed http://dx.doi.org/10.4056/sigs.3858183
Article
PubMed Central
PubMed
Google Scholar
Buddruhs N, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, et al. Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a member of the Roseobacter clade. Stand Genomic Sci 2013; 9:128–141. PubMed http://dx.doi.org/10.4056/sigs.4297965
Article
PubMed Central
PubMed
Google Scholar
Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 2004; 432:910–913. PubMed http://dx.doi.org/10.1038/nature03170
Article
CAS
PubMed
Google Scholar
Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 2012; 7:e34846. PubMed http://dx.doi.org/10.1371/journal.pone.0034846
Article
PubMed Central
CAS
PubMed
Google Scholar
Vaas LAI, Sikorski J, Hofner B, Buddruhs N, Fiebig A, Klenk HP, Göker M. opm: An R package for analysing OmniLog® Phenotype MicroArray Data. Bioinformatics 2013; 29:1823–1824. PubMed http://dx.doi.org/10.1093/bioinformatics/btt291
Article
CAS
PubMed
Google Scholar
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence(MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360
Article
PubMed Central
CAS
PubMed
Google Scholar
Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mzrachi I, et al. Clarifying Concepts and Terms in Biodiversity Informatics. PLoS Biol 2011; 9:e1001088. PubMed http://dx.doi.org/10.1371/journal.pbio.1001088
Article
PubMed Central
CAS
PubMed
Google Scholar
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
Article
PubMed Central
CAS
PubMed
Google Scholar
Garrity G, Bell J, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Brenner D, Krieg N, Staley J, Garrity G, eds. Bergey’s Manual of Systematic Bacteriology, Vol. 2 Part B The Gammaproteobacteria. Second Edition. New York: Springer; 2005:1.
Chapter
Google Scholar
Garrity G, Bell J, Lilburn T. Class I. Alphaproteobacteria class. nov. In: Garrity G, Brenner D, Krieg N, Staley J, eds. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part C. Second Edition. New York: Springer; 2005:1.
Chapter
Google Scholar
Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1–6. PubMed http://dx.doi.org/10.1099/ijs.0.64188-0
Garrity G, Bellm J, Lilburn T. Order III. Rhodobacterales ord. nov. In: Garrity G, Brenner D, Krieg N, Staley J, eds. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part C. Second Edition. New York: Springer; 2005:161.
Google Scholar
Garrity GM, Bell JA, Lilburn T. Family III. Rhodobacteraceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, eds. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part C. Second Edition. New York: Springer; 2005:161.
Google Scholar
Yoon JH, Kang SJ, Lee SY, Oh TK. Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2007; 57:856–861. PubMed http://dx.doi.org/10.1099/ijs.0.64779-0
Article
CAS
PubMed
Google Scholar
BAuA. 2010, Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 168, p.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556
Article
PubMed Central
CAS
PubMed
Google Scholar
List of growth media at the DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/list-of-media-for-microorganisms.html
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
Article
PubMed Central
PubMed
Google Scholar
Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 2009; 1:63–67. PubMed http://dx.doi.org/10.4056/sigs.632
Article
PubMed Central
PubMed
Google Scholar
Zhang S, Meyer R. The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer. Mol Microbiol 1997; 25:509–516. PubMed http://dx.doi.org/10.1046/j.1365-2958.1997.4861849.x
Article
CAS
PubMed
Google Scholar
Colby J, Stirling DI, Dalton H. The soluble methane mono-oxygenase of Methylococcus capsulatus (Bath). Its ability to oxygenate n-alkanes, n-alkenes, ethers, and alicyclic, aromatic and heterocyclic compounds. Biochem J 1977; 165:395–402. PubMed
Article
PubMed Central
CAS
PubMed
Google Scholar
Schilling B, Lerch K. Cloning, sequencing and heterologous expression of the monoamine oxidase gene from Aspergillus niger. Mol Gen Genet 1995; 247:430–438. PubMed http://dx.doi.org/10.1007/BF00293144
Article
CAS
PubMed
Google Scholar
Cumby N, Davidson AR, Maxwell KL. The moron comes of age. Bacteriophage 2012; 2:225–228. PubMed http://dx.doi.org/10.4161/bact.23146
Article
PubMed Central
PubMed
Google Scholar
Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH. Crystal structure of the ATP-binding subunit of an ABC transporter. Nature 1998; 396:703–707. PubMed http://dx.doi.org/10.1038/25393
Article
CAS
PubMed
Google Scholar
Langille MGI, Brinkman FSL. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009; 25:664–665. PubMed http://dx.doi.org/10.1093/bioinformatics/btp030
Article
PubMed Central
CAS
PubMed
Google Scholar
Langille MG, Hsiao WWL, Brinkman FSL. Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008; 9:329. PubMed http://dx.doi.org/10.1186/1471-2105-9-329
Article
PubMed Central
PubMed
Google Scholar
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovik K, Meinicke P, Merkl R. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006; 7:142. PubMed http://dx.doi.org/10.1186/1471-2105-7-142
Article
PubMed Central
PubMed
Google Scholar
Hsiao W, Wan I, Jones SJ, Brinkman FSL. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003; 19:418–420. PubMed http://dx.doi.org/10.1093/bioinformatics/btg004
Article
CAS
PubMed
Google Scholar
del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejes R. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 1998; 62:434–464. PubMed
PubMed Central
PubMed
Google Scholar
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: A fast phage search tool. Nucleic Acids Res 2011; 39:W347–W352. PubMed http://dx.doi.org/10.1093/nar/gkr485
Article
PubMed Central
CAS
PubMed
Google Scholar
Biers EJ, Wang K, Pennington C, Belas R, Chen F, Moran MA. Occurrence and expression of gene transfer agent genes in marine bacterioplankton. Appl Environ Microbiol 2008; 74:2933–2939. PubMed http://dx.doi.org/10.1128/AEM.02129-07
Article
PubMed Central
CAS
PubMed
Google Scholar
Harrison PW, Lower RPJ, Kim NKD, Young JPW. Introducing the bacterial “chromid”: not a chromosome, not a plasmid. Trends Microbiol 2010; 18:141–148. PubMed http://dx.doi.org/10.1016/j.tim.2009.12.010
Article
CAS
PubMed
Google Scholar
Petersen J, Frank O, Göker M, Pradella S. Extrachromosomal, extraordinary and essential-the plasmids of the Roseobacter clade. Appl Microbiol Biotechnol 2013; 97:2805–2815. PubMed http://dx.doi.org/10.1007/s00253-013-4746-8
Article
CAS
PubMed
Google Scholar
Petersen J, Brinkmann H, Berger M, Brinkhoff T, Päuker O, Pradella S. Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales. Mol Biol Evol 2011; 28:1229–1240. PubMed http://dx.doi.org/10.1093/molbev/msq310
Article
CAS
PubMed
Google Scholar
Petersen J, Brinkmann H, Pradella S. Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 2009; 11:2627–2638. PubMed http://dx.doi.org/10.1111/j.1462-2920.2009.01987.x
Article
CAS
PubMed
Google Scholar
Bartosik D, Wlodarczyk M, Thomas CM. Complete nucleotide sequence of the replicator region of Paracoccus (Thiobacillus) versutus pTAV1 plasmid and its correlation to several plasmids of Agrobacterium and Rhizobium species. Plasmid 1997; 38:53–59. PubMed http://dx.doi.org/10.1006/plas.1997.1295
Article
CAS
PubMed
Google Scholar
Petersen J. Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 2011; 193:313–321. PubMed
CAS
PubMed
Google Scholar
Cascales E, Christie PJ. The versatile bacterial type IV secretion systems. Nat Rev Microbiol 2003; 1:137–149. PubMed http://dx.doi.org/10.1038/nrmicro753
Article
CAS
PubMed
Google Scholar
Zielenkiewicz U, Ceglowski P. Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. Acta Biochim Pol 2001; 48:1003–1023. PubMed
CAS
PubMed
Google Scholar
R Development Core Team. R: A language and evironment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria 2008. ISBN 3-900051-07-0.
Google Scholar
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006; 22:1540–1542. PubMed http://dx.doi.org/10.1093/bioinformatics/btl117
Article
CAS
PubMed
Google Scholar
Neilands JB. Siderophores: Structure and Function of Microbial Iron Transport Compounds. J Biol Chem 1995; 270:26723–26726. PubMed http://dx.doi.org/10.1074/jbc.270.45.26723
Article
CAS
PubMed
Google Scholar
Geng H, Bruhn JB, Nielsen KF, Gram L, Belas R. Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters. Appl Environ Microbiol 2008; 74:1535–1545. PubMed http://dx.doi.org/10.1128/AEM.02339-07
Article
PubMed Central
CAS
PubMed
Google Scholar
Lally ET, Hill RB, Kieba IR, Korostoff J. The interaction between RTX toxins and target cells. Trends Microbiol 1999; 7:356–361. PubMed http://dx.doi.org/10.1016/S0966-842X(99)01530-9
Article
CAS
PubMed
Google Scholar
Giraud MF, Naismith JH. The rhamnose pathway. Curr Opin Struct Biol 2000; 10:687–696. PubMed http://dx.doi.org/10.1016/S0959-440X(00)00145-7
Article
CAS
PubMed
Google Scholar
Ravin NV. N15: the linear phage-plasmid. Plasmid 2011; 65:102–109. PubMed http://dx.doi.org/10.1016/j.plasmid.2010.12.004
Article
CAS
PubMed
Google Scholar
Rybchin VN, Svarchevsky AN. The plasmid prophage N15: a linear DNA with covalently closed ends. Mol Microbiol 1999; 33:895–903. PubMed http://dx.doi.org/10.1046/j.1365-2958.1999.01533.x
Article
CAS
PubMed
Google Scholar
Kumari A, Pasini P, Deo SK, Flomenhoft D, Shashidhar S, Daunert S. Biosensing Systems for the Detection of Bacterial Quorum Signaling Molecules. Anal Chem 2006; 78:7603–7609. PubMed http://dx.doi.org/10.1021/ac061421n
Article
CAS
PubMed
Google Scholar
Collins AJ, Nyholm SV. Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes. J Bacteriol 2011; 193:3397–3398. PubMed http://dx.doi.org/10.1128/JB.05139-11
Article
PubMed Central
CAS
PubMed
Google Scholar
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60. PubMed http://dx.doi.org/10.1186/1471-2105-1460
Article
PubMed Central
PubMed
Google Scholar
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464. http://dx.doi.org/10.1099/00207713-37-4-463
Article
Google Scholar
Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266. PubMed http://dx.doi.org/10.1099/ijs.0.016949-0
Article
CAS
PubMed
Google Scholar
Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, et al. The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010; 2010:690737. PubMed http://dx.doi.org/10.1155/2010/690737
Article
PubMed Central
PubMed
Google Scholar
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
Article
CAS
PubMed
Google Scholar
Göker M, Scheuner C, Klenk HP, Stielow JB, Menzel W. Codivergence of Mycoviruses with Their Hosts. PLoS ONE 2011; 6:e22252. PubMed http://dx.doi.org/10.1371/journal.pone.0022252
Article
PubMed Central
PubMed
Google Scholar
Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, et al. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci 2012; 6:194–209. PubMed http://dx.doi.org/10.4056/sigs.2796069
Article
PubMed Central
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402. PubMed http://dx.doi.org/10.1093/nar/25.17.3389
Article
PubMed Central
CAS
PubMed
Google Scholar
Enright AJ, Van Dongen SM, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002; 30:1575–1584. PubMed http://dx.doi.org/10.1093/nar/30.7.1575
Article
PubMed Central
CAS
PubMed
Google Scholar
Li L, Stoeckert CJ, Jr., Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189. PubMed http://dx.doi.org/10.1101/gr.1224503
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797. PubMed http://dx.doi.org/10.1093/nar/gkh340
Article
PubMed Central
CAS
PubMed
Google Scholar
Thompson JD, Thierry JCC, Poch O. RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics 2003; 19:1155–1161. PubMed http://dx.doi.org/10.1093/bioinformatics/btg133
Article
CAS
PubMed
Google Scholar
Meusemann K, Von Reumont BM, Simon S, Roeding F, Strauss S, Kück P, Ebersberger I, Walzl M, Pass G, Breuers S, et al. A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol 2010; 27:2451–2464. PubMed http://dx.doi.org/10.1093/molbev/msq130
Article
CAS
PubMed
Google Scholar
Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376. PubMed http://dx.doi.org/10.1007/BF01734359
Article
CAS
PubMed
Google Scholar
Fitch WM. Toward defining the course of evolution: minimum change on a specified tree topology. Syst Zool 1971; 20:406–416. http://dx.doi.org/10.2307/2412116
Article
Google Scholar
Goloboff PA. Parsimony, likelihood, and simplicity. Cladistics 2003; 19:91–103. http://dx.doi.org/10.1111/j.1096-0031.2003.tb00297.x
Article
Google Scholar
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690. PubMed http://dx.doi.org/10.1093/bioinformatics/btl446
Article
CAS
PubMed
Google Scholar
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758–771. PubMed http://dx.doi.org/10.1080/10635150802429642
Article
PubMed
Google Scholar
Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Association, MA: Sunderland, 2002.
Google Scholar
Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides NC. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS ONE 2011; 6:e20237. PubMed http://dx.doi.org/10.1371/journal.pone.0020237
Article
PubMed Central
CAS
PubMed
Google Scholar
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669–674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
Article
Google Scholar
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? J Comput Biol 2010; 17:337–354. PubMed http://dx.doi.org/10.1089/cmb.2009.0179
Article
CAS
PubMed
Google Scholar