Phylogenetic data
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In this study, we utilize the genome-wide singlenucleotide polymorphisms (SNPs) data obtained through Multiplexed Inter Simple Sequence Repeat Genotyping by sequencing (MIG-seq) to explore the phylogenetic relationships among Quercus species in Vietnam. The results of this study reveal that all Quercus species in Vietnam belong to subgenus Cerris and the phylogenetic analysis strongly supports the recognition of two infrageneric sections: Quercus and Ilex section for the Vietnamese Quercus.
10p dianmotminh02 03-05-2024 2 1 Download
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Ebook "Introduction to computational biology: An evolutionary approach" Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models.
329p tracanhphuonghoa1007 22-04-2024 10 2 Download
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The present study aims to identify Neofusicoccum isolates collected from lotus with symptoms of dieback, blight, and wilted leaves. Species were identified based on their morphology and comparison of the DNA sequence data for ITS rDNA and β-tubulin (tub-2). The taxonomy and phylogenetic relationships of pathogen isolates were investigated, and their pathogenic abilities were determined.
17p viritesh 02-04-2024 5 1 Download
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A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret wholegenome sequencing data for genotypic drug susceptibility testing (DST).
8p vibransone 28-03-2024 3 2 Download
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Ebook The families and genera of vascular plants - Volume XIII: Flowering plants, monocots (Poaceae)
Ebook "The families and genera of vascular plants - Volume XIII: Flowering plants, monocots (Poaceae)" is the outcome of a modern phylogenetic analysis of the grass family based on multiple sources of data, in particular molecular systematic studies resulting from a concerted effort by researchers worldwide, including the author. In the classification given here grasses are subdivided into 12 subfamilies with 29 tribes and over 700 genera. The keys and descriptions for the taxa above the rank of genus are hierarchical, i.e.
413p manmanthanhla0201 26-02-2024 3 1 Download
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Ebook "Morphometries: Applications in Biology and Paleontology" with the quantitative characterization and analysis of morphological data, students increasingly see morphometrics as a necessary complement to molecular studies in their quests to understand the origin and maintenance of biodiversity. Moreover, morphometrics has recently been shown to have direct utility in phylogenetic contexts, by both finding new, and sharpening the definition of old, character states.
269p manmanthanhla0201 27-02-2024 1 1 Download
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The study using molecular data from three DNA regions (matK, rbcL, and trnH-psbA) supported the monophyly of Melodinus. The M. cochinchinensis from Vietnam and China are closely related. There are some genetic variations in the sequences of Melodinus cochinchinensis from Belgium versus Asiatic M. cochinchinensis, as well as the phylogenetic position of the species, suggesting the possibility of misidentification of M. cochinchinensis from Belgium.
7p giangnhanly 02-10-2023 8 3 Download
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Phytoplankton species composition, abundance, biodiversity indices and their influence by environmental conditions were examined in Thi Nai lagoon using data from four surveys in 2004, 2008, 2009 and 2020. A total of 367 taxa of phytoplankton belonging to ten groups was recorded, of which diatoms were dominant with over 60% of the total species.
20p vicaptainmarvel 21-04-2023 6 2 Download
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The present study, based on the molecular data of seven DNA regions supported the relationship within the genus Altingia. Three clades were recognized in this genus. The species A. excelsa from Lao Cai province of Vietnam was well supported as closely related to A. siamensis by molecular data, this result is congruent with morphology, and distribution.
8p vimalfoy 08-02-2023 4 1 Download
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The genus Sphagnum is one of the richest taxa among the Turkish bryophytes. Up to now, it has been represented by 27 taxa in six sections (Sphagnum, Acutifolia, Squarrosa, Subsecunda, Cuspidata, and Rigida). In this study, an identification key for the section Sphagnum was prepared, and the section was investigated using phylogenetic analyses, with a main focus on Turkish bryophytes. This study provides the first sequence data of the trnL intron region for five species of the section Sphagnum from Turkey (namely S. centrale, S. divinum, S. medium, S. palustre, and S.
10p lyhuyenthu 31-01-2023 4 2 Download
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Inocybe viscida sp. nov., a novel species found in a forest with old trees of Pinus brutia and tertiary relict endemic Liquidambar orientalis in coastal area of southwestern Turkey, is described and illustrated. We present this new species based on morphological and molecular data from nuclear rDNA internal transcribed spacer region (ITS1-5.8SITS2 = ITS) and the portions of nuc 28S rRNA (LSU) gene. Comprehensive description, field photographs, line drawings of the microscopic features and comparisons with phenetically similar taxa and phylogenetically related species are discussed.
11p lyhuyenthu 31-01-2023 9 2 Download
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In this paper, we show a detailed look at the barley XTH gene family, including detailed bioinformatics analyses of conserved protein motifs and structure, phylogenetic relationships, and a comparison of the expression patterns during germination and seedling growth using RT-qPCR and RNA-Seq analyses. Overall, there was a good correlation between RT-qPCR and RNA-Seq data for similar tissues. RNA-Seq data showed many different expression profile patterns, from broad, high level expression for some XTH genes to highly tissue specific patterns for others.
17p lyhuyenthu 31-01-2023 6 2 Download
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The most recent research projects in scientifc feld of eutherian comparative genomics included intentions to sequence every extant eutherian species genome in foreseeable future, so that future revisions and updates of eutherian gene data sets were expected.
4p vihagrid 30-01-2023 11 3 Download
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A small rhacophorid, Philautus petilus known from only the female holotype, is recorded for the first time outside of the type locality in Laos. Three specimens, containing the first known males of the species, were collected from Muong Nhe Nature Reserve in Dien Bien Province, northwestern Vietnam. The Vietnamese specimens are identified as P. petilus based on morphological similarities with the holotype from Laos. In addition, our molecular data verify the transfer of this species from Philautus to the genus Theloderma.
9p runordie3 27-06-2022 8 2 Download
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The phylogenetic relationship of 83 taxa of Santalaceae s.l. was reconstructed based on the molecular data sets including the nuclear ribosomal (small and large subunit rDNA) and the chloroplast rbcL, matK, and trnL-F regions. The Maximum likelihood (ML) and Bayesian inference (BI) methods were used to build the phylogenetic trees.
8p viellenkullman 13-05-2022 6 1 Download
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Exploring the phylogenetic relationships between taxa provides important information for science. The phylogenetic study of Macrosolen was conducted based on molecular data sets of 27 taxa with five DNA regions including chloroplast rbcL, matK, and trnL-F and nuclear ribosomal (small subunit rDNA and large subunit rDNA) regions to reconstruct the phylogenetic relationship of Macrosolen.
7p viginnirometty 04-05-2022 17 1 Download
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Phylogenetically informed distances are commonly used in the analysis of microbiome data, and analysts have many options to choose from. Although all phylogenetic distances share the goal of incorporating the phylogenetic relationships among the bacteria, they do so in different ways and give different pictures of the relationships between the bacterial communities.
16p vigalileogalilei 27-02-2022 10 1 Download
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Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multilocus sequencing typing, have not been quantified.
6p vielonmusk 30-01-2022 45 0 Download
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Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-sites models.
20p vialfrednobel 29-01-2022 5 0 Download
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Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells.
14p viaristotle 29-01-2022 13 0 Download