Genome-based phylogenetic analysis
Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis
... and phylogenetic analysis allow for discovery of more phylogenetically informative and stable targets that can be used in rapid, relatively simple assays (28, 50, ...canSNPs based on WGS to classify ...
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Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis
... comparative phylogenetic strategy, we were able to identify molecular evolutionary correlates between genetic variation and MLS and other primate life-history ...one based on the detection of parallel ...
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MRSA Transmission on a Neonatal Intensive Care Unit: Epidemiological and Genome-Based Phylogenetic Analyses
... S3). Phylogenetic analysis on the basis of detected SNPs indicated that 28 isolates formed a strongly supported monophyletic clade (Figure 2, Figure S1), confirming close epidemiological linkage between ...
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A SNP based phylogenetic analysis of Corynebacterium diphtheriae in Malaysia
... whole genome SNP analysis in our study by comparing the SNPs in core genome and pan-genome which includes the full complement of bacterial genes: core genome and dispensable ...
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Molecular characterization and phylogenetic analysis of the complete genome of a porcine sapovirus from Chinese swine
... The porcine SaV strain in the present study came from an outbreak of gastroenteritis in piglets group, which had inserted sequence at the 3' end of ORF2. The role of the inserted sequence was unknown, but it is highly ...
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Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia
... Note, the F gene-based rRT-PCR assays are different or specific to the two HMPV groups. Discussion HMPV causes respiratory illness presenting as mild upper respiratory tract infection or life-threatening se- vere ...
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Estimating phylogenetic trees from genome-scale data
... in phylogenetic analysis, such as long branch attraction (Table1) 29 ...is based on at most a few thousand base pairs, which may be small enough such that departures from stationarity may be less ...
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Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome
... Comparisons based on gene numbers are a better in which all the genes have been isolated from the ge- test of genome complexity than those based on DNA nomes of both a vertebrate and a basal ...
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Phylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole Genome Sequencing Data
... PGG and SCG analysis. Of the 66 isolates sequenced, 57 could be assigned to a PGG based on sequence data, as shown in Fig. 3A. Four isolates clustered within PGG1, 31 clustered within PGG2, and 22 clustered ...
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Recombination analysis based on the complete genome of bocavirus
... Abstract Bocavirus include bovine parvovirus, minute virus of canine, porcine bocavirus, gorilla bocavirus, and Human bocaviruses 1-4 (HBoVs). Although recent reports showed that recombination happened in bocavirus, no ...
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The First Mitochondrial Genome for Caddisfly (Insecta: Trichoptera) with Phylogenetic Implications
... Phryganeidae). Firstly, considering the structure of mt genome, the cox1 of the two caddisfly species (E. re- gina and Apatania sp.) herein studied both start with CGA (coding for R), and all lepidopteran species ...
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Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference
... Sankoff and Blanchette [7] introduced the first algorithmic approach to the reconstruction of a phylo- genetic tree from whole-genome data, BPAnalysis. The algorithm seeks the tree and internal genomes which ...
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The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes
... phylogeny based on complete chloroplast genomes In a landmark article that included data from multiple sources, the Grass Phylogeny Working Group [13] exam- ined relationships among grasses using a large and ...
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Phylogenetic Analysis of Non O157 Shiga Toxin Producing Escherichia coli Strains by Whole Genome Sequencing
... Genomic analysis re- vealed that O111:NM strain DEC12C carried fliC for the H2 ...tree based on whole-genome-wide SNPs was performed with 10,000 iterations by TNT (tree analysis using new ...
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Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early genotype phylogenetic position and recent genotype genome size
... the phylogenetic tree based on the entire genome sequences of the five F48-like NDVs in this study and those of other NDVs representing geno- types I through VIII which are available from the Gen- ...
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Phylogenetic analysis of the complete mitochondrial genome of madurella mycetomatis confirms its taxonomic position within the order sordariales
... mycetomatis has been discovered, the taxonomic classification of Madurella has long been a challenge. Especially, since there are also no asexual conidia produced nor other morphological and ultractructural characters ...
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Comparative Assessment of Performance and Genome Dependence among Phylogenetic Profiling Methods
... inadequate genome diversity were unsuccessful, previous research utilizing the structure of the phylogenetic tree while making functional predictions indicates that this may be at least part of the problem ...
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Comparative assessment of performance and genome dependence among phylogenetic profiling methods
... an analysis of the effectiveness of applying phylo- genetic profiling to eukaryotes has yet to be studied in lit- erature, homology based methods of generating profiles for prokaryotes has been presented in ...
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Phylogenetic Relationships within the Tribe Hippotragini (Antilopinae: Bovidae) Based on Mitochondrial Genome
... the phylogenetic trees, except for COXI, Addax nasomaculatus is considered as a sister group for the monophyletic group of the genus ...Also, based on the whole mitogenomes, the extinct blaubok ...close ...
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New approach for phylogenetic tree recovery based on genome-scale metabolic networks
... two phylogenetic trees that we have ...of phylogenetic tree reconstruction is the ...reduced genome with around almost a thousand metabolites, several hundred metabolites will not have a ...
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