GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas
Authors
Keywords
-
Journal
Frontiers in Microbiology
Volume 9, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2018-05-01
DOI
10.3389/fmicb.2018.00771
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia
- (2018) Luisa Sandner-Miranda et al. Frontiers in Microbiology
- A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter
- (2017) Julie Jeukens et al. Genome Biology and Evolution
- Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace
- (2017) Grady Weyenberg et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Transfer of Pseudomonas pictorum Gray and Thornton 1928 to genus Stenotrophomonas as Stenotrophomonas pictorum comb. nov., and emended description of the genus Stenotrophomonas
- (2017) Aboubakar Sidiki Ouattara et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations
- (2017) Iván Sánchez-Castro et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
- (2017) Matthew B Parks et al. MOLECULAR BIOLOGY AND EVOLUTION
- ModelFinder: fast model selection for accurate phylogenetic estimates
- (2017) Subha Kalyaanamoorthy et al. NATURE METHODS
- Simplified and representative bacterial community of maize roots
- (2017) Ben Niu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Clustal Omega for making accurate alignments of many protein sequences
- (2017) Fabian Sievers et al. PROTEIN SCIENCE
- Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
- (2017) Sean P. Gordon et al. Nature Communications
- Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management
- (2017) Elizabeth A Savory et al. eLife
- Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups
- (2017) Guillermo Nourdin-Galindo et al. Frontiers in Cellular and Infection Microbiology
- Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex
- (2017) Luz E. Ochoa-Sánchez et al. Frontiers in Microbiology
- Double-Face Meets the Bacterial World: The Opportunistic Pathogen Stenotrophomonas maltophilia
- (2017) Felipe Lira et al. Frontiers in Microbiology
- Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex
- (2017) Jeff Gauthier et al. Frontiers in Microbiology
- Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis
- (2017) Margarita Gomila et al. Frontiers in Microbiology
- Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species
- (2017) Bruno Contreras-Moreira et al. Frontiers in Plant Science
- Contentious relationships in phylogenomic studies can be driven by a handful of genes
- (2017) Xing-Xing Shen et al. Nature Ecology & Evolution
- Simultaneous Cr(VI) reduction and Zn(II) biosorption by Stenotrophomonas sp. and constitutive expression of related genes
- (2016) Shimei Ge et al. BIOTECHNOLOGY LETTERS
- Gene content dissimilarity for subclassification of highly similar microbial strains
- (2016) Qichao Tu et al. BMC GENOMICS
- Gene flow, recombination, and positive selection in Stenotrophomonas maltophilia: mechanisms underlying the diversity of the widespread opportunistic pathogen
- (2016) Dong Yu et al. GENOME
- Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus
- (2016) Yutaka Handa et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties
- (2016) Amélie Deredjian et al. RESEARCH IN MICROBIOLOGY
- Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa
- (2016) Vartul Sangal et al. Scientific Reports
- Genome Sequence of Type Strains of Genus Stenotrophomonas
- (2016) Prashant P. Patil et al. Frontiers in Microbiology
- Biodegradation of DDT by Stenotrophomonas sp. DDT-1: Characterization and genome functional analysis
- (2016) Xiong Pan et al. Scientific Reports
- Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia
- (2015) Theodore R. Pak et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- MeDuSa: a multi-draft based scaffolder
- (2015) Emanuele Bosi et al. BIOINFORMATICS
- Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm
- (2015) Aurélia Caputo et al. Biology Direct
- Comparative Genomics of Environmental and ClinicalStenotrophomonas maltophiliaStrains with Different Antibiotic Resistance Profiles
- (2015) Benjamin Youenou et al. Genome Biology and Evolution
- Past and future species definitions for Bacteria and Archaea
- (2015) Ramon Rosselló-Móra et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Microbial Speciation
- (2015) B. Jesse Shapiro et al. Cold Spring Harbor Perspectives in Biology
- A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
- (2015) David J. Roach et al. PLoS Genetics
- Update on infections caused by Stenotrophomonas maltophilia with particular attention to resistance mechanisms and therapeutic options
- (2015) Ya-Ting Chang et al. Frontiers in Microbiology
- Friends or foes: can we make a distinction between beneficial and harmful strains of the Stenotrophomonas maltophilia complex?
- (2015) Gabriele Berg et al. Frontiers in Microbiology
- Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients
- (2015) Kate L. Ormerod et al. PeerJ
- Time to revisit polyphasic taxonomy
- (2014) Peter Vandamme et al. ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
- kdetrees: non-parametric estimation of phylogenetic tree distributions
- (2014) Grady Weyenberg et al. BIOINFORMATICS
- Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria
- (2014) Peyman Alavi et al. BMC GENOMICS
- Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus
- (2014) Vincent P. Richards et al. Genome Biology and Evolution
- Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
- (2014) J. Chun et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Virulence genes in clinical and environmental Stenotrophomas maltophilia isolates: A genome sequencing and gene expression approach
- (2014) Martina Adamek et al. MICROBIAL PATHOGENESIS
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Recombination Blurs Phylogenetic Groups Routine Assignment in Escherichia coli: Setting the Record Straight
- (2014) María-Carmen Turrientes et al. PLoS One
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- PhyloSift: phylogenetic analysis of genomes and metagenomes
- (2014) Aaron E. Darling et al. PeerJ
- GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
- (2013) Bruno Contreras-Moreira et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Microbial genomic taxonomy
- (2013) Cristiane C Thompson et al. BMC GENOMICS
- MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING
- (2013) James B. Pease et al. EVOLUTION
- Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters
- (2013) Ruth E. Timme et al. Genome Biology and Evolution
- Inferring ancient divergences requires genes with strong phylogenetic signals
- (2013) Leonidas Salichos et al. NATURE
- ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R
- (2012) Andrei-Alin Popescu et al. BIOINFORMATICS
- Stenotrophomonas maltophilia: an Emerging Global Opportunistic Pathogen
- (2012) J. S. Brooke CLINICAL MICROBIOLOGY REVIEWS
- Genome Sequence of Stenotrophomonas maltophilia RR-10, Isolated as an Endophyte from Rice Root
- (2012) B. Zhu et al. JOURNAL OF BACTERIOLOGY
- Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain
- (2012) F. Lira et al. JOURNAL OF BACTERIOLOGY
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
- (2012) Julien Soubrier et al. MOLECULAR BIOLOGY AND EVOLUTION
- Population Genomics of Early Events in the Ecological Differentiation of Bacteria
- (2012) B. J. Shapiro et al. SCIENCE
- Patterns of Gene Flow Define Species of Thermophilic Archaea
- (2012) Hinsby Cadillo-Quiroz et al. PLOS BIOLOGY
- Stenotrophomonas interspecies differentiation and identification by gyrB sequence analysis
- (2011) Liselott A. Svensson-Stadler et al. FEMS MICROBIOLOGY LETTERS
- Statistics and Truth in Phylogenomics
- (2011) S. Kumar et al. MOLECULAR BIOLOGY AND EVOLUTION
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- (2011) F. Sievers et al. Molecular Systems Biology
- Genotyping of Environmental and Clinical Stenotrophomonas maltophilia Isolates and their Pathogenic Potential
- (2011) Martina Adamek et al. PLoS One
- Delineation of Stenotrophomonas spp. by multi-locus sequence analysis and MALDI-TOF mass spectrometry
- (2011) Zinaida Vasileuskaya-Schulz et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Characterizing the Phylogenetic Tree-Search Problem
- (2011) Daniel Money et al. SYSTEMATIC BIOLOGY
- Screening for endophytic nitrogen-fixing bacteria in Brazilian sugar cane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov.
- (2010) P. L. Ramos et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Stenotrophomonas daejeonensis sp. nov., isolated from sewage
- (2010) M. Lee et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field
- (2010) Hoonbok Yi et al. JOURNAL OF MICROBIOLOGY
- Comparison of 61 Sequenced Escherichia coli Genomes
- (2010) Oksana Lukjancenko et al. MICROBIAL ECOLOGY
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
- (2010) Stéphane Guindon et al. SYSTEMATIC BIOLOGY
- Impact of recombination on bacterial evolution
- (2010) Xavier Didelot et al. TRENDS IN MICROBIOLOGY
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Genomic taxonomy of vibrios
- (2009) Cristiane C Thompson et al. BMC EVOLUTIONARY BIOLOGY
- Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field
- (2009) H.-B. Kim et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- A Stenotrophomonas maltophilia Multilocus Sequence Typing Scheme for Inferring Population Structure
- (2009) S. Kaiser et al. JOURNAL OF BACTERIOLOGY
- The versatility and adaptation of bacteria from the genus Stenotrophomonas
- (2009) Robert P. Ryan et al. NATURE REVIEWS MICROBIOLOGY
- Shifting the genomic gold standard for the prokaryotic species definition
- (2009) Michael Richter et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium
- (2009) Elena Kaparullina et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Gene tree discordance, phylogenetic inference and the multispecies coalescent
- (2009) James H. Degnan et al. TRENDS IN ECOLOGY & EVOLUTION
- Genetic Structures at the Origin of Acquisition of the -Lactamase blaKPC Gene
- (2008) T. Naas et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees
- (2008) S. Taghavi et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent
- (2008) P. Vinuesa et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation
- (2008) Samuel V. Angiuoli et al. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
- Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
- (2008) A. Koeppel et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A simple, fast, and accurate method of phylogenomic inference
- (2008) Martin Wu et al. GENOME BIOLOGY
- The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants
- (2008) Lisa C Crossman et al. GENOME BIOLOGY
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started