Cargando…

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from la...

Descripción completa

Detalles Bibliográficos
Autores principales:	Edwards, David J., Duchene, Sebastián, Pope, Bernard, Holt, Kathryn E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Microbiology Society 2021
Materias:	Research Articles
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8767352/ https://www.ncbi.nlm.nih.gov/pubmed/34874243 http://dx.doi.org/10.1099/mgen.0.000694

Ejemplares similares

HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
por: Crispell, Joseph, et al.
Publicado: (2019)

Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis Lineages
por: Outhred, Alexander C., et al.
Publicado: (2020)

Evolution of Bcl-2 homology motifs: homology versus homoplasy
por: Aouacheria, Abdel, et al.
Publicado: (2013)

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution
por: Van Damme, Kay, et al.
Publicado: (2021)

Homoplasy in the evolution of modern human-like joint proportions in Australopithecus afarensis
por: Prabhat, Anjali M, et al.
Publicado: (2021)

Homoplasy as an Auxiliary Criterion for Species Delimitation
por: Conti, Angela, et al.
Publicado: (2021)

Homoplasy of Retrotransposon Insertions in Toothed Whales
por: Doronina, Liliya, et al.
Publicado: (2023)

Suspected cases of intracontinental Burkholderia pseudomallei sequence type homoplasy resolved using whole-genome sequencing
por: Aziz, Ammar, et al.
Publicado: (2017)

Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10
por: Anmarkrud, Jarl A, et al.
Publicado: (2008)

Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species
por: Dickey, Aaron M, et al.
Publicado: (2013)

Convergent evolution of animal and microbial rhodopsins
por: Kojima, Keiichi, et al.
Publicado: (2023)

Selaginella Genome Analysis – Entering the “Homoplasy Heaven” of the MADS World
por: Gramzow, Lydia, et al.
Publicado: (2012)

Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy
por: De Smet, Birgit, et al.
Publicado: (2014)

Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference
por: Schull, James K, et al.
Publicado: (2022)

Updated site concordance factors minimize effects of homoplasy and taxon sampling
por: Mo, Yu K, et al.
Publicado: (2022)

Correction: Convergent evolution of animal and microbial rhodopsins
por: Kojima, Keiichi, et al.
Publicado: (2023)

Osteological Variation among Extreme Morphological Forms in the Mexican Salamander Genus Chiropterotriton (Amphibia: Plethodontidae): Morphological Evolution And Homoplasy
por: Darda, David M., et al.
Publicado: (2015)

Impact of insertion sequences on convergent evolution of Shigella species
por: Hawkey, Jane, et al.
Publicado: (2020)

Amplified fragment length homoplasy: in silico analysis for model and non-model species
por: Paris, Margot, et al.
Publicado: (2010)

Appropriate homoplasy metrics in linked SSRs to predict an underestimation of demographic expansion times
por: Ortega-Del Vecchyo, Diego, et al.
Publicado: (2017)

Quantifying the extent of morphological homoplasy: A phylogenetic analysis of 490 characters in Drosophila
por: Al Sayad, Sinan, et al.
Publicado: (2019)

Mitogenomic phylogeny of Typhlocybinae (Hemiptera: Cicadellidae) reveals homoplasy in tribal diagnostic morphological traits
por: Yan, Bin, et al.
Publicado: (2022)

Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective
por: Mason-Gamer, Roberta J
Publicado: (2007)

Molecular Phylogeny of the Astrophorida (Porifera, Demospongiae (p)) Reveals an Unexpected High Level of Spicule Homoplasy
por: Cárdenas, Paco, et al.
Publicado: (2011)

Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages
por: Chen, Heidi I., et al.
Publicado: (2023)

Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages
por: Chen, Heidi I, et al.
Publicado: (2023)

Convergent algorithms for protein structural alignment
por: Martínez, Leandro, et al.
Publicado: (2007)

Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene
por: Schobel, Seth A., et al.
Publicado: (2016)

Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation
por: Gort, Gerrit, et al.
Publicado: (2009)

When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus)
por: Henriques, Romina, et al.
Publicado: (2016)

Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes
por: Lai, Yi-Pin, et al.
Publicado: (2020)

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae, Conflicting with Current Classification Schemes
por: Wu, Zeng-Yuan, et al.
Publicado: (2015)

Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance
por: Coolen, Jordy P. M., et al.
Publicado: (2021)

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections
por: Giulieri, Stefano G, et al.
Publicado: (2022)

Convergent evolution in the Euarchontoglires
por: Morris, Philip J. R., et al.
Publicado: (2018)

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
por: Rogozin, Igor B, et al.
Publicado: (2008)

Evolutionary history of the fish genus Astyanax Baird & Girard (1854) (Actinopterygii, Characidae) in Mesoamerica reveals multiple morphological homoplasies
por: Ornelas-García, Claudia Patricia, et al.
Publicado: (2008)

Convergence of ESP with other disciplines
por: Stojkovic, Nadezda, et al.
Publicado: (2018)

Whole-brain modelling identifies distinct but convergent paths to unconsciousness in anaesthesia and disorders of consciousness
por: Luppi, Andrea I., et al.
Publicado: (2022)

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks
por: Frith, Martin C., et al.
Publicado: (2008)

Cannot write session to /tmp/vufind_sessions/sess_2u7dm2g8rn1900ib41abphrest