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Phylogenetic Analysis of Bacterial Pathogen Genomes
The development of high-throughput sequencing technology has led to a significant reduction in the time and cost of sequencing whole genomes of...
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Introduction to Phylogenetic Analysis of Molecular Sequence Data
Phylogeny is a model of the relationships between organisms, genes, proteins, or other structures based on common ancestry. It is also used for...
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Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel
In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient...
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Tangent Phylogenetic PCA
Phylogenetic PCA (p-PCA) is a version of PCA for observations that are leaf nodes of a phylogenetic tree. P-PCA accounts for the fact that such...
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Gene characterization and phylogenetic analysis of four mitochondrial genomes in Caenogastropoda
Caenogastropoda is a highly diverse group, containing ∼60% of all existing gastropods. Species in this subclass predominantly inhabit marine...
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PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data
BackgroundUnderstanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and...
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Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis
ObjectiveDiversification of cell types and changes in epigenetic states during cell differentiation processes are important for understanding...
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Phylogenetic analysis of Lamiaceae based on transcriptome data
The Lamiaceae family is included in the angiosperms and comprises over 7000 species, many of which are of considerable ecological, economic, and...
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Assigning Taxonomy, Building Phylogenetic Tree
Taxonomic classification of the representative sequences and clustering of OTUs (Operational Taxonomic Units) are two core steps in bioinformatic...
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Methods for Rich Phylogenetic Inference Over Distributed Sexual Populations
The structure of relatedness among members of an evolved population tells much of its evolutionary history. In application-oriented evolutionary...
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Taxonomy and phylogenetic diversity among the yeasts
Yeasts are among the economically and scientifically most important eukaryotic microorganisms known. At present, there are 1,500 recognized species,...
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Investigating pigeon circovirus infection in a pigeon farm: molecular detection, phylogenetic analysis and complete genome analysis
BackgroundPigeon circovirus infections in pigeons ( Columba livia domestica ) have been reported worldwide. Pigeons should be PiCV-free when utilized...
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Comparative mitochondrial genome analysis of Cynoglossidae (Teleost: Pleuronectiformes) and phylogenetic implications
Generally, a teleostean group (e.g., family or genus) owns one type or a set of similar mitochondrial gene arrangement. It is interesting, however,...
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A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins
Because of the limited effectiveness of prevailing phylogenetic methods when applied to highly divergent protein sequences, the phylogenetic analysis...
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Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae)
Oreomecon nudicaulis , commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis , which was previously...
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The complete chloroplast genome of Mussaenda pubescens and phylogenetic analysis
The chloroplast (cp) genome sequence of Mussaenda pubescens , a promising resource that is used as a traditional medicine and drink, is important for...
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DeepBiome: A Phylogenetic Tree Informed Deep Neural Network for Microbiome Data Analysis
Evidence linking the microbiome to human health is rapidly growing. The microbiome profile has the potential as a novel predictive biomarker for many...
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Bayesian phylogenetic analysis of Philippine languages supports a rapid migration of Malayo-Polynesian languages
The Philippines are central to understanding the expansion of the Austronesian language family from its homeland in Taiwan. It remains unknown to...
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Comparative genome and phylogenetic analysis revealed the complex mitochondrial genome and phylogenetic position of Conopomorpha sinensis Bradley
Conopomorpha sinensis Bradley is a destructive pest that causes severe economic damage to litchi and longan. Previous C. sinensis research has...
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DNA Barcoding and Phylogenetic Analysis of Ceylon Oak with Other Fruit Plants in Sapindaceae Family
Ceylon oak ( Schleichera oleosa (Lour.) Oken), belonging to Sapindaceae family, is a widely used plant for its medicinal properties. Currently, few...
